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smoke-tests.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns ="http://www.w3.org/1999/xhtml"><head><meta content="text/html;charset=utf-8" http-equiv="Content-Type"/><title>Cucumber</title><style type="text/css">/* cucumber.css is generated from cucumber.sass */
/* Regenerate with rake sass */
body {
font-size: 0px;
color: white;
margin: 0px;
padding: 0px;
}
.cucumber, td, th {
font: normal 11px "Lucida Grande", Helvetica, sans-serif;
background: white;
color: black;
}
.cucumber #cucumber-header, td #cucumber-header, th #cucumber-header {
background: #65c400;
color: white;
height: 6em;
}
.cucumber #cucumber-header #expand-collapse p, td #cucumber-header #expand-collapse p, th #cucumber-header #expand-collapse p {
float: right;
margin: 0 0 0 10px;
}
.cucumber .scenario h3, td .scenario h3, th .scenario h3, .background h3 {
font-size: 11px;
padding: 3px;
margin: 0;
background: #65c400;
color: white;
font-weight: bold;
}
.background h3 {
font-size: 1.2em;
background: #666;
}
.cucumber h1, td h1, th h1 {
margin: 0px 10px 0px 10px;
padding: 10px;
font-family: "Lucida Grande", Helvetica, sans-serif;
font-size: 2em;
position: absolute;
}
.cucumber h4, td h4, th h4 {
margin-bottom: 2px;
}
.cucumber div.feature, td div.feature, th div.feature {
padding: 2px;
margin: 0px 10px 5px 10px;
}
.cucumber div.examples, td div.examples, th div.examples {
padding: 0em 0em 0em 1em;
}
.cucumber .stats, td .stats, th .stats {
margin: 2em;
}
.cucumber .summary ul.features li, td .summary ul.features li, th .summary ul.features li {
display: inline;
}
.cucumber .step_name, td .step_name, th .step_name {
float: left;
}
.cucumber .step_file, td .step_file, th .step_file {
text-align: right;
color: #999999;
}
.cucumber .step_file a, td .step_file a, th .step_file a {
color: #999999;
}
.cucumber .scenario_file, td .scenario_file, th .scenario_file {
float: right;
color: #999999;
}
.cucumber .tag, td .tag, th .tag {
font-weight: bold;
color: #246ac1;
}
.cucumber .backtrace, td .backtrace, th .backtrace {
margin-top: 0;
margin-bottom: 0;
margin-left: 1em;
color: black;
}
.cucumber a, td a, th a {
text-decoration: none;
color: #be5c00;
}
.cucumber a:hover, td a:hover, th a:hover {
text-decoration: underline;
}
.cucumber a:visited, td a:visited, th a:visited {
font-weight: normal;
}
.cucumber a div.examples, td a div.examples, th a div.examples {
margin: 5px 0px 5px 15px;
color: black;
}
.cucumber .outline table, td .outline table, th .outline table {
margin: 0px 0px 5px 10px;
}
.cucumber table, td table, th table {
border-collapse: collapse;
}
.cucumber table td, td table td, th table td {
padding: 3px 3px 3px 5px;
}
.cucumber table td.failed, .cucumber table td.passed, .cucumber table td.skipped, .cucumber table td.pending, .cucumber table td.undefined, td table td.failed, td table td.passed, td table td.skipped, td table td.pending, td table td.undefined, th table td.failed, th table td.passed, th table td.skipped, th table td.pending, th table td.undefined {
padding-left: 18px;
padding-right: 10px;
}
.cucumber table td.failed, td table td.failed, th table td.failed {
border-left: 5px solid #c20000;
border-bottom: 1px solid #c20000;
background: #fffbd3;
color: #c20000;
}
.cucumber table td.passed, td table td.passed, th table td.passed {
border-left: 5px solid #65c400;
border-bottom: 1px solid #65c400;
background: #dbffb4;
color: #3d7700;
}
.cucumber table td.skipped, td table td.skipped, th table td.skipped {
border-left: 5px solid aqua;
border-bottom: 1px solid aqua;
background: #e0ffff;
color: #001111;
}
.cucumber table td.pending, td table td.pending, th table td.pending {
border-left: 5px solid #faf834;
border-bottom: 1px solid #faf834;
background: #fcfb98;
color: #131313;
}
.cucumber table td.undefined, td table td.undefined, th table td.undefined {
border-left: 5px solid #faf834;
border-bottom: 1px solid #faf834;
background: #fcfb98;
color: #131313;
}
.cucumber table td.message, td table td.message, th table td.message {
border-left: 5px solid aqua;
border-bottom: 1px solid aqua;
background: #e0ffff;
color: #001111;
}
.cucumber ol, td ol, th ol {
list-style: none;
margin: 0px;
padding: 0px;
}
.cucumber ol li.step, td ol li.step, th ol li.step {
padding: 3px 3px 3px 18px;
margin: 5px 0px 5px 5px;
}
.cucumber ol li, td ol li, th ol li {
margin: 0em 0em 0em 1em;
padding: 0em 0em 0em 0.2em;
}
.cucumber ol li span.param, td ol li span.param, th ol li span.param {
font-weight: bold;
}
.cucumber ol li.failed, td ol li.failed, th ol li.failed {
border-left: 5px solid #c20000;
border-bottom: 1px solid #c20000;
background: #fffbd3;
color: #c20000;
}
.cucumber ol li.passed, td ol li.passed, th ol li.passed {
border-left: 5px solid #65c400;
border-bottom: 1px solid #65c400;
background: #dbffb4;
color: #3d7700;
}
.cucumber ol li.skipped, td ol li.skipped, th ol li.skipped {
border-left: 5px solid aqua;
border-bottom: 1px solid aqua;
background: #e0ffff;
color: #001111;
}
.cucumber ol li.pending, td ol li.pending, th ol li.pending {
border-left: 5px solid #faf834;
border-bottom: 1px solid #faf834;
background: #fcfb98;
color: #131313;
}
.cucumber ol li.undefined, td ol li.undefined, th ol li.undefined {
border-left: 5px solid #faf834;
border-bottom: 1px solid #faf834;
background: #fcfb98;
color: #131313;
}
.cucumber ol li.message, td ol li.message, th ol li.message {
border-left: 5px solid aqua;
border-bottom: 1px solid aqua;
background: #e0ffff;
color: #001111;
margin-left: 10px;
}
.cucumber #summary, td #summary, th #summary {
margin: 0px;
padding: 5px 10px;
text-align: right;
top: 0px;
right: 0px;
float: right;
}
.cucumber #summary p, td #summary p, th #summary p {
margin: 0 0 0 2px;
}
.cucumber #summary #totals, td #summary #totals, th #summary #totals {
font-size: 1.2em;
}
.ruby {
font-size: 12px;
font-family: monospace;
color: white;
background: black;
padding: 0.1em 0 0.2em 0;
}
.ruby .keyword {
color: #ff6600;
}
.ruby .constant {
color: #339999;
}
.ruby .attribute {
color: white;
}
.ruby .global {
color: white;
}
.ruby .module {
color: white;
}
.ruby .class {
color: white;
}
.ruby .string {
color: #66ff00;
}
.ruby .ident {
color: white;
}
.ruby .method {
color: #ffcc00;
}
.ruby .number {
color: white;
}
.ruby .char {
color: white;
}
.ruby .comment {
color: #9933cc;
}
.ruby .symbol {
color: white;
}
.ruby .regex {
color: #44b4cc;
}
.ruby .punct {
color: white;
}
.ruby .escape {
color: white;
}
.ruby .interp {
color: white;
}
.ruby .expr {
color: white;
}
.ruby .offending {
background: #333333;
}
.ruby .linenum {
width: 75px;
padding: 0.1em 1em 0.2em 0;
color: black;
background: #fffbd3;
}
</style><script type="text/javascript">/*!
* jQuery JavaScript Library v1.4.2
* http://jquery.com/
*
* Copyright 2010, John Resig
* Dual licensed under the MIT or GPL Version 2 licenses.
* http://jquery.org/license
*
* Includes Sizzle.js
* http://sizzlejs.com/
* Copyright 2010, The Dojo Foundation
* Released under the MIT, BSD, and GPL Licenses.
*
* Date: Sat Feb 13 22:33:48 2010 -0500
*/
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SCENARIOS = "h3[id^='scenario_'],h3[id^=background_]";
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function moveProgressBar(percentDone) {
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</script></head><body><!-- Step count 913--><div class="cucumber"><div id="cucumber-header"><div id="label"><h1>Cucumber Features</h1></div><div id="summary"><p id="totals"></p><p id="duration"></p><div id="expand-collapse"><p id="expander">Expand All</p><p id="collapser">Collapse All</p></div></div></div><div class="feature"><h2><span class="val">Feature: assign-confidence</span></h2><p class="narrative">assign-confidence evaluates the statistical confidence for each PSMs obtained<br/>from tide-search.<br/></p><div class='scenario outline'><span class="scenario_file">features/assign-confidence.feature:5</span><h3 id="scenario_1"><span class="keyword">Scenario Outline:</span> <span class="val">User runs tide-index / tide-search</span></h3><ol><li id='features_assign-confidence_feature_6' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('0.1');</script><li id='features_assign-confidence_feature_7' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('0.2');</script><li id='features_assign-confidence_feature_8' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments --overwrite T --seed 7 <args> <input></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('0.3');</script><li id='features_assign-confidence_feature_9' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run assign-confidence</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('0.4');</script><li id='features_assign-confidence_feature_10' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('0.5');</script><li id='features_assign-confidence_feature_11' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/<actual_output> should contain the same lines as good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:41</span></div></li> <script type="text/javascript">moveProgressBar('0.6');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_14'><th class="step skipped_param" id="row_14_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_14_1"><div><span class="step param">args</span></div></th><th class="step skipped_param" id="row_14_2"><div><span class="step param">input</span></div></th><th class="step skipped_param" id="row_14_3"><div><span class="step param">actual_output</span></div></th><th class="step skipped_param" id="row_14_4"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('0.7');</script><tr class='step' id='row_15'><td class="step passed" id="row_15_0"><div><span class="step param">xcorr</span></div></td><td class="step passed" id="row_15_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_15_2"><div><span class="step param">assign-default.target.txt</span></div></td><td class="step passed" id="row_15_3"><div><span class="step param">assign-confidence.target.txt</span></div></td><td class="step passed" id="row_15_4"><div><span class="step param">assign-confidence-default.target.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('0.8');</script><tr class='step' id='row_16'><td class="step passed" id="row_16_0"><div><span class="step param">concat</span></div></td><td class="step passed" id="row_16_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_16_2"><div><span class="step param">assign-concat.txt</span></div></td><td class="step passed" id="row_16_3"><div><span class="step param">assign-confidence.target.txt</span></div></td><td class="step passed" id="row_16_4"><div><span class="step param">assign-confidence-concat.target.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('0.9');</script><tr class='step' id='row_17'><td class="step passed" id="row_17_0"><div><span class="step param">auto-score</span></div></td><td class="step passed" id="row_17_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_17_2"><div><span class="step param">assign-exactpval.target.txt</span></div></td><td class="step passed" id="row_17_3"><div><span class="step param">assign-confidence.target.txt</span></div></td><td class="step passed" id="row_17_4"><div><span class="step param">assign-confidence-exact-tdc.target.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('1.0');</script><tr class='step' id='row_18'><td class="step passed" id="row_18_0"><div><span class="step param">exact_pval</span></div></td><td class="step passed" id="row_18_1"><div><span class="step param">--score "exact p-value"</span></div></td><td class="step passed" id="row_18_2"><div><span class="step param">assign-exactpval.target.txt</span></div></td><td class="step passed" id="row_18_3"><div><span class="step param">assign-confidence.target.txt</span></div></td><td class="step passed" id="row_18_4"><div><span class="step param">assign-confidence-exact-tdc.target.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('1.2');</script><tr class='step' id='row_19'><td class="step passed" id="row_19_0"><div><span class="step param">exact_pval_mixmax</span></div></td><td class="step passed" id="row_19_1"><div><span class="step param">--score "exact p-value" --estimation-method mix-max</span></div></td><td class="step passed" id="row_19_2"><div><span class="step param">assign-exactpval.target.txt</span></div></td><td class="step passed" id="row_19_3"><div><span class="step param">assign-confidence.target.txt</span></div></td><td class="step passed" id="row_19_4"><div><span class="step param">assign-confidence-mixmax.target.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('1.3');</script><tr class='step' id='row_20'><td class="step passed" id="row_20_0"><div><span class="step param">sidak</span></div></td><td class="step passed" id="row_20_1"><div><span class="step param">--score "exact p-value" --sidak T</span></div></td><td class="step passed" id="row_20_2"><div><span class="step param">assign-exactpval.target.txt</span></div></td><td class="step passed" id="row_20_3"><div><span class="step param">assign-confidence.target.txt</span></div></td><td class="step passed" id="row_20_4"><div><span class="step param">assign-confidence-sidak.target.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('1.4');</script><tr class='step' id='row_21'><td class="step passed" id="row_21_0"><div><span class="step param">peptide-level</span></div></td><td class="step passed" id="row_21_1"><div><span class="step param">--score "exact p-value" --estimation-method peptide-level</span></div></td><td class="step passed" id="row_21_2"><div><span class="step param">assign-exactpval.target.txt</span></div></td><td class="step passed" id="row_21_3"><div><span class="step param">assign-confidence.target.txt</span></div></td><td class="step passed" id="row_21_4"><div><span class="step param">assign-confidence-peptidelevel.target.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('1.5');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: barista</span></h2><p class="narrative">barista should re-rank a collection of PSMs using the barista algorithm<br/></p><div class='scenario outline'><span class="scenario_file">features/barista.feature:4</span><h3 id="scenario_2"><span class="keyword">Scenario Outline:</span> <span class="val">User runs barista</span></h3><ol><li id='features_barista_feature_5' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('1.6');</script><li id='features_barista_feature_6' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('1.7');</script><li id='features_barista_feature_7' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments --overwrite T <args> <spectra> <search_results></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('1.8');</script><li id='features_barista_feature_8' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run barista</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('1.9');</script><li id='features_barista_feature_9' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('2.0');</script><li id='features_barista_feature_10' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/<actual_output> should match good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:37</span></div></li> <script type="text/javascript">moveProgressBar('2.1');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_13'><th class="step skipped_param" id="row_13_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_13_1"><div><span class="step param">args</span></div></th><th class="step skipped_param" id="row_13_2"><div><span class="step param">spectra</span></div></th><th class="step skipped_param" id="row_13_3"><div><span class="step param">search_results</span></div></th><th class="step skipped_param" id="row_13_4"><div><span class="step param">actual_output</span></div></th><th class="step skipped_param" id="row_13_5"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('2.3');</script><tr class='step' id='row_14'><td class="step passed" id="row_14_0"><div><span class="step param">barista-simple</span></div></td><td class="step passed" id="row_14_1"><div><span class="step param">--separate-searches barista-args/barista-tide-search.decoy.txt barista-args/barista-concat.fasta</span></div></td><td class="step passed" id="row_14_2"><div><span class="step param">barista-args/barista-demo.ms2</span></div></td><td class="step passed" id="row_14_3"><div><span class="step param">barista-args/barista-tide-search.target.txt</span></div></td><td class="step passed" id="row_14_4"><div><span class="step param">barista.target.psms.txt</span></div></td><td class="step passed" id="row_14_5"><div><span class="step param">barista-barista.target.psms.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('2.4');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: bullseye</span></h2><p class="narrative">bullseye should assign high resolution precursor m/z values to MS/MS data<br/>using the Hardklor algorithm<br/></p><div class='scenario outline'><span class="scenario_file">features/bullseye.feature:5</span><h3 id="scenario_3"><span class="keyword">Scenario Outline:</span> <span class="val">User runs bullseye</span></h3><ol><li id='features_bullseye_feature_6' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('2.5');</script><li id='features_bullseye_feature_7' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('2.6');</script><li id='features_bullseye_feature_8' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments --overwrite T --parameter-file <param_file> <ms1_spectra> <ms2_spectra></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('2.7');</script><li id='features_bullseye_feature_9' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run bullseye</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('2.8');</script><li id='features_bullseye_feature_10' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('2.9');</script><li id='features_bullseye_feature_11' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/bullseye.pid.ms2 should match good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:37</span></div></li> <script type="text/javascript">moveProgressBar('3.0');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_14'><th class="step skipped_param" id="row_14_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_14_1"><div><span class="step param">param_file</span></div></th><th class="step skipped_param" id="row_14_2"><div><span class="step param">ms1_spectra</span></div></th><th class="step skipped_param" id="row_14_3"><div><span class="step param">ms2_spectra</span></div></th><th class="step skipped_param" id="row_14_4"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('3.1');</script><tr class='step' id='row_15'><td class="step passed" id="row_15_0"><div><span class="step param">bullseye-default</span></div></td><td class="step passed" id="row_15_1"><div><span class="step param">params/default-bullseye</span></div></td><td class="step passed" id="row_15_2"><div><span class="step param">hardklor.test.ms1</span></div></td><td class="step passed" id="row_15_3"><div><span class="step param">bullseye.test.ms2</span></div></td><td class="step passed" id="row_15_4"><div><span class="step param">bullseye.pid.ms2</span></div></td></tr> <script type="text/javascript">moveProgressBar('3.2');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: tide-index / cascade-search</span></h2><p class="narrative">tide-index should create an index for all peptides in a fasta file, for use in<br/>subsequent calls to tide-search<br/>cascade-search should search a collection of spectra against a sequence database,<br/>returning a collection of peptide-spectrum matches (PSMs)<br/></p><div class='scenario outline'><span class="scenario_file">features/cascade-search.feature:7</span><h3 id="scenario_4"><span class="keyword">Scenario Outline:</span> <span class="val">User runs tide-index / cascade-search</span></h3><ol><li id='features_cascade-search_feature_8' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('3.3');</script><li id='features_cascade-search_feature_9' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('3.5');</script><li id='features_cascade-search_feature_10' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments --overwrite T small-yeast.fasta small_yeast_index</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('3.6');</script><li id='features_cascade-search_feature_11' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run tide-index as an intermediate step</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:25</span></div></li> <script type="text/javascript">moveProgressBar('3.7');</script><li id='features_cascade-search_feature_12' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('3.8');</script><li id='features_cascade-search_feature_13' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments --overwrite T --missed-cleavages 1 small-yeast.fasta small_yeast_index_mc1</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('3.9');</script><li id='features_cascade-search_feature_14' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run tide-index as an intermediate step</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:25</span></div></li> <script type="text/javascript">moveProgressBar('4.0');</script><li id='features_cascade-search_feature_15' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('4.1');</script><li id='features_cascade-search_feature_16' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments --overwrite T <search_args> <spectra> <index></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('4.2');</script><li id='features_cascade-search_feature_17' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run cascade-search</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('4.3');</script><li id='features_cascade-search_feature_18' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('4.4');</script><li id='features_cascade-search_feature_19' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/<actual_output> should contain the same lines as good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:41</span></div></li> <script type="text/javascript">moveProgressBar('4.6');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_23'><th class="step skipped_param" id="row_23_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_23_1"><div><span class="step param">search_args</span></div></th><th class="step skipped_param" id="row_23_2"><div><span class="step param">index</span></div></th><th class="step skipped_param" id="row_23_3"><div><span class="step param">spectra</span></div></th><th class="step skipped_param" id="row_23_4"><div><span class="step param">actual_output</span></div></th><th class="step skipped_param" id="row_23_5"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('4.7');</script><tr class='step' id='row_24'><td class="step passed" id="row_24_0"><div><span class="step param">cascade-default</span></div></td><td class="step passed" id="row_24_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_24_2"><div><span class="step param">small_yeast_index</span></div></td><td class="step passed" id="row_24_3"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_24_4"><div><span class="step param">cascade-search.target.txt</span></div></td><td class="step passed" id="row_24_5"><div><span class="step param">cascade-default.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('4.8');</script><tr class='step' id='row_25'><td class="step passed" id="row_25_0"><div><span class="step param">cascade-2-index</span></div></td><td class="step passed" id="row_25_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_25_2"><div><span class="step param">small_yeast_index,small_yeast_index_mc1</span></div></td><td class="step passed" id="row_25_3"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_25_4"><div><span class="step param">cascade-search.target.txt</span></div></td><td class="step passed" id="row_25_5"><div><span class="step param">cascade-2-index.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('4.9');</script><tr class='step' id='row_26'><td class="step passed" id="row_26_0"><div><span class="step param">cascade-q-value</span></div></td><td class="step passed" id="row_26_1"><div><span class="step param">--q-value-threshold 0.0005</span></div></td><td class="step passed" id="row_26_2"><div><span class="step param">small_yeast_index,small_yeast_index_mc1</span></div></td><td class="step passed" id="row_26_3"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_26_4"><div><span class="step param">cascade-search.target.txt</span></div></td><td class="step passed" id="row_26_5"><div><span class="step param">cascade-q-value.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('5.0');</script><tr class='step' id='row_27'><td class="step passed" id="row_27_0"><div><span class="step param">cascade-min-max</span></div></td><td class="step passed" id="row_27_1"><div><span class="step param">--estimation-method min-max</span></div></td><td class="step passed" id="row_27_2"><div><span class="step param">small_yeast_index,small_yeast_index_mc1</span></div></td><td class="step passed" id="row_27_3"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_27_4"><div><span class="step param">cascade-search.target.txt</span></div></td><td class="step passed" id="row_27_5"><div><span class="step param">cascade-min-max.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('5.1');</script><tr class='step' id='row_28'><td class="step passed" id="row_28_0"><div><span class="step param">cascade-pep-lvl</span></div></td><td class="step passed" id="row_28_1"><div><span class="step param">--estimation-method peptide-level</span></div></td><td class="step passed" id="row_28_2"><div><span class="step param">small_yeast_index,small_yeast_index_mc1</span></div></td><td class="step passed" id="row_28_3"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_28_4"><div><span class="step param">cascade-search.target.txt</span></div></td><td class="step passed" id="row_28_5"><div><span class="step param">cascade-pep-lvl.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('5.2');</script><tr class='step' id='row_29'><td class="step passed" id="row_29_0"><div><span class="step param">cascade-extpval</span></div></td><td class="step passed" id="row_29_1"><div><span class="step param">--score "exact p-value" --exact-p-value T</span></div></td><td class="step passed" id="row_29_2"><div><span class="step param">small_yeast_index,small_yeast_index_mc1</span></div></td><td class="step passed" id="row_29_3"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_29_4"><div><span class="step param">cascade-search.target.txt</span></div></td><td class="step passed" id="row_29_5"><div><span class="step param">cascade-extpval.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('5.3');</script><tr class='step' id='row_30'><td class="step passed" id="row_30_0"><div><span class="step param">cascade-sidak</span></div></td><td class="step passed" id="row_30_1"><div><span class="step param">--score "exact p-value" --exact-p-value T --sidak T</span></div></td><td class="step passed" id="row_30_2"><div><span class="step param">small_yeast_index,small_yeast_index_mc1</span></div></td><td class="step passed" id="row_30_3"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_30_4"><div><span class="step param">cascade-search.target.txt</span></div></td><td class="step passed" id="row_30_5"><div><span class="step param">cascade-sidak.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('5.4');</script><tr class='step' id='row_31'><td class="step passed" id="row_31_0"><div><span class="step param">cascade-comb-cs</span></div></td><td class="step passed" id="row_31_1"><div><span class="step param">--estimation-method peptide-level --combine-charge-states T</span></div></td><td class="step passed" id="row_31_2"><div><span class="step param">small_yeast_index,small_yeast_index_mc1</span></div></td><td class="step passed" id="row_31_3"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_31_4"><div><span class="step param">cascade-search.target.txt</span></div></td><td class="step passed" id="row_31_5"><div><span class="step param">cascade-comb-cs.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('5.5');</script><tr class='step' id='row_32'><td class="step passed" id="row_32_0"><div><span class="step param">cascade-comb-mp</span></div></td><td class="step passed" id="row_32_1"><div><span class="step param">--estimation-method peptide-level --combine-modified-peptides T</span></div></td><td class="step passed" id="row_32_2"><div><span class="step param">small_yeast_index,small_yeast_index_mc1</span></div></td><td class="step passed" id="row_32_3"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_32_4"><div><span class="step param">cascade-search.target.txt</span></div></td><td class="step passed" id="row_32_5"><div><span class="step param">cascade-comb-mp.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('5.6');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: comet</span></h2><p class="narrative">comet should search a collection of spectra against a sequence database<br/>returning a collection of PSMs<br/></p><div class='scenario outline'><span class="scenario_file">features/comet.feature:5</span><h3 id="scenario_5"><span class="keyword">Scenario Outline:</span> <span class="val">User runs comet</span></h3><ol><li id='features_comet_feature_6' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('5.8');</script><li id='features_comet_feature_7' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('5.9');</script><li id='features_comet_feature_8' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments --overwrite T --parameter-file <param_file> test_spectra/<spectra> test_databases/<fasta></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('6.0');</script><li id='features_comet_feature_9' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run comet</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('6.1');</script><li id='features_comet_feature_10' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('6.2');</script><li id='features_comet_feature_11' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/comet.target.txt should match good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:37</span></div></li> <script type="text/javascript">moveProgressBar('6.3');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_14'><th class="step skipped_param" id="row_14_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_14_1"><div><span class="step param">param_file</span></div></th><th class="step skipped_param" id="row_14_2"><div><span class="step param">spectra</span></div></th><th class="step skipped_param" id="row_14_3"><div><span class="step param">fasta</span></div></th><th class="step skipped_param" id="row_14_4"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('6.4');</script><tr class='step' id='row_15'><td class="step passed" id="row_15_0"><div><span class="step param">comet_autodecoy</span></div></td><td class="step passed" id="row_15_1"><div><span class="step param">params/comet_autodecoy</span></div></td><td class="step passed" id="row_15_2"><div><span class="step param">JE102306_102306_18Mix4_Tube1_01.ms2</span></div></td><td class="step passed" id="row_15_3"><div><span class="step param">comet_autodecoy.fasta</span></div></td><td class="step passed" id="row_15_4"><div><span class="step param">comet_autodecoy.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('6.5');</script><tr class='step' id='row_16'><td class="step passed" id="row_16_0"><div><span class="step param">comet_autodecoy1</span></div></td><td class="step passed" id="row_16_1"><div><span class="step param">params/comet_autodecoy1</span></div></td><td class="step passed" id="row_16_2"><div><span class="step param">JE102306_102306_18Mix4_Tube1_01.ms2</span></div></td><td class="step passed" id="row_16_3"><div><span class="step param">comet_autodecoy.fasta</span></div></td><td class="step passed" id="row_16_4"><div><span class="step param">comet_autodecoy1.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('6.6');</script><tr class='step' id='row_17'><td class="step passed" id="row_17_0"><div><span class="step param">comet_binarymod2</span></div></td><td class="step passed" id="row_17_1"><div><span class="step param">params/comet_binarymod2</span></div></td><td class="step passed" id="row_17_2"><div><span class="step param">sh_1617_JX_070209p_KO410_run2.ms2</span></div></td><td class="step passed" id="row_17_3"><div><span class="step param">comet_binarymod2.fasta</span></div></td><td class="step passed" id="row_17_4"><div><span class="step param">comet_binarymod2.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('6.7');</script><tr class='step' id='row_18'><td class="step passed" id="row_18_0"><div><span class="step param">comet_binarymods</span></div></td><td class="step passed" id="row_18_1"><div><span class="step param">params/comet_binarymods</span></div></td><td class="step passed" id="row_18_2"><div><span class="step param">sh_1617_JX_070209p_KO410_run2.ms2</span></div></td><td class="step passed" id="row_18_3"><div><span class="step param">comet_binarymods.fasta</span></div></td><td class="step passed" id="row_18_4"><div><span class="step param">comet_binarymods.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('6.9');</script><tr class='step' id='row_19'><td class="step passed" id="row_19_0"><div><span class="step param">comet_commandline</span></div></td><td class="step passed" id="row_19_1"><div><span class="step param">params/comet_commandline</span></div></td><td class="step passed" id="row_19_2"><div><span class="step param">sh_1617_JX_070209p_KO410_run2.ms2</span></div></td><td class="step passed" id="row_19_3"><div><span class="step param">comet_plain.fasta</span></div></td><td class="step passed" id="row_19_4"><div><span class="step param">comet_commandline.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('7.0');</script><tr class='step' id='row_20'><td class="step passed" id="row_20_0"><div><span class="step param">comet_ctermmod</span></div></td><td class="step passed" id="row_20_1"><div><span class="step param">params/comet_ctermmod</span></div></td><td class="step passed" id="row_20_2"><div><span class="step param">sh_1617_JX_070209p_KO410_run1.ms2</span></div></td><td class="step passed" id="row_20_3"><div><span class="step param">comet_term-mod.fasta</span></div></td><td class="step passed" id="row_20_4"><div><span class="step param">comet_ctermmod.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('7.1');</script><tr class='step' id='row_21'><td class="step passed" id="row_21_0"><div><span class="step param">comet_noenzyme</span></div></td><td class="step passed" id="row_21_1"><div><span class="step param">params/comet_noenzyme</span></div></td><td class="step passed" id="row_21_2"><div><span class="step param">sh_1617_JX_070209p_KO410_run1.ms2</span></div></td><td class="step passed" id="row_21_3"><div><span class="step param">comet_noenzyme.fasta</span></div></td><td class="step passed" id="row_21_4"><div><span class="step param">comet_noenzyme.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('7.2');</script><tr class='step' id='row_22'><td class="step passed" id="row_22_0"><div><span class="step param">comet_plain</span></div></td><td class="step passed" id="row_22_1"><div><span class="step param">params/comet_plain</span></div></td><td class="step passed" id="row_22_2"><div><span class="step param">sh_1617_JX_070209p_KO410_run2.ms2</span></div></td><td class="step passed" id="row_22_3"><div><span class="step param">comet_plain.fasta</span></div></td><td class="step passed" id="row_22_4"><div><span class="step param">comet_plain.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('7.3');</script><tr class='step' id='row_23'><td class="step passed" id="row_23_0"><div><span class="step param">comet_semi-tryptic</span></div></td><td class="step passed" id="row_23_1"><div><span class="step param">params/comet_semi-tryptic</span></div></td><td class="step passed" id="row_23_2"><div><span class="step param">sh_1617_JX_070209p_KO410_run1.ms2</span></div></td><td class="step passed" id="row_23_3"><div><span class="step param">comet_tryptic.fasta</span></div></td><td class="step passed" id="row_23_4"><div><span class="step param">comet_semi-tryptic.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('7.4');</script><tr class='step' id='row_24'><td class="step passed" id="row_24_0"><div><span class="step param">comet_stop-codon</span></div></td><td class="step passed" id="row_24_1"><div><span class="step param">params/comet_stop-codon</span></div></td><td class="step passed" id="row_24_2"><div><span class="step param">sh_1617_JX_070209p_KO410_run2.ms2</span></div></td><td class="step passed" id="row_24_3"><div><span class="step param">comet_stop-codon.fasta</span></div></td><td class="step passed" id="row_24_4"><div><span class="step param">comet_stop-codon.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('7.5');</script><tr class='step' id='row_25'><td class="step passed" id="row_25_0"><div><span class="step param">comet_term-mod</span></div></td><td class="step passed" id="row_25_1"><div><span class="step param">params/comet_term-mod</span></div></td><td class="step passed" id="row_25_2"><div><span class="step param">sh_1617_JX_070209p_KO410_run1.ms2</span></div></td><td class="step passed" id="row_25_3"><div><span class="step param">comet_term-mod.fasta</span></div></td><td class="step passed" id="row_25_4"><div><span class="step param">comet_term-mod.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('7.6');</script><tr class='step' id='row_26'><td class="step passed" id="row_26_0"><div><span class="step param">comet_term-mod2</span></div></td><td class="step passed" id="row_26_1"><div><span class="step param">params/comet_noenzyme</span></div></td><td class="step passed" id="row_26_2"><div><span class="step param">sh_1617_JX_070209p_KO410_run1.ms2</span></div></td><td class="step passed" id="row_26_3"><div><span class="step param">comet_term-mod.fasta</span></div></td><td class="step passed" id="row_26_4"><div><span class="step param">comet_term-mod2.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('7.7');</script><tr class='step' id='row_27'><td class="step passed" id="row_27_0"><div><span class="step param">comet_tryptic</span></div></td><td class="step passed" id="row_27_1"><div><span class="step param">params/comet_tryptic</span></div></td><td class="step passed" id="row_27_2"><div><span class="step param">sh_1617_JX_070209p_KO410_run1.ms2</span></div></td><td class="step passed" id="row_27_3"><div><span class="step param">comet_tryptic.fasta</span></div></td><td class="step passed" id="row_27_4"><div><span class="step param">comet_tryptic.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('7.8');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: generate-peptides</span></h2><p class="narrative">generate-peptides should extract from a given set of protein sequences a list<br/>of target and decoy peptides fitting the specified criteria<br/></p><div class='scenario outline'><span class="scenario_file">features/generate-peptides.feature:5</span><h3 id="scenario_6"><span class="keyword">Scenario Outline:</span> <span class="val">User runs generate-peptides</span></h3><ol><li id='features_generate-peptides_feature_6' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('7.9');</script><li id='features_generate-peptides_feature_7' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('8.1');</script><li id='features_generate-peptides_feature_8' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments <args></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('8.2');</script><li id='features_generate-peptides_feature_9' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run generate-peptides</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('8.3');</script><li id='features_generate-peptides_feature_10' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('8.4');</script><li id='features_generate-peptides_feature_11' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/generate-peptides.target.txt should match good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:37</span></div></li> <script type="text/javascript">moveProgressBar('8.5');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_14'><th class="step skipped_param" id="row_14_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_14_1"><div><span class="step param">args</span></div></th><th class="step skipped_param" id="row_14_2"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('8.6');</script><tr class='step' id='row_15'><td class="step passed" id="row_15_0"><div><span class="step param">generate_peptides_default</span></div></td><td class="step passed" id="row_15_1"><div><span class="step param">--overwrite T test.fasta</span></div></td><td class="step passed" id="row_15_2"><div><span class="step param">standard_generate_peptides_default.out</span></div></td></tr> <script type="text/javascript">moveProgressBar('8.7');</script><tr class='step' id='row_16'><td class="step passed" id="row_16_0"><div><span class="step param">generate_peptides_specifying_miss_cleavages</span></div></td><td class="step passed" id="row_16_1"><div><span class="step param">--parameter-file params/params_uniq test.fasta</span></div></td><td class="step passed" id="row_16_2"><div><span class="step param">standard_generate_peptides_specifying_missed_cleavages.out</span></div></td></tr> <script type="text/javascript">moveProgressBar('8.8');</script><tr class='step' id='row_17'><td class="step passed" id="row_17_0"><div><span class="step param">generate_peptides_change_minmax</span></div></td><td class="step passed" id="row_17_1"><div><span class="step param">--parameter-file params/many_changes test.fasta</span></div></td><td class="step passed" id="row_17_2"><div><span class="step param">standard_generate_peptides_change_minmax</span></div></td></tr> <script type="text/javascript">moveProgressBar('8.9');</script><tr class='step' id='row_18'><td class="step passed" id="row_18_0"><div><span class="step param">generate_peptides_chymo</span></div></td><td class="step passed" id="row_18_1"><div><span class="step param">--parameter-file params/chymo test.fasta</span></div></td><td class="step passed" id="row_18_2"><div><span class="step param">standard_generate_peptides_chymo</span></div></td></tr> <script type="text/javascript">moveProgressBar('9.0');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: get-ms2-spectrum</span></h2><p class="narrative">get-ms2-spectrum should extract one or more fragmentation spectra, specified<br/>by scan number, from an MS2 file<br/></p><div class='scenario outline'><span class="scenario_file">features/get-ms2-spectrum.feature:5</span><h3 id="scenario_7"><span class="keyword">Scenario Outline:</span> <span class="val">User runs get-ms2-spectrum</span></h3><ol><li id='features_get-ms2-spectrum_feature_6' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('9.2');</script><li id='features_get-ms2-spectrum_feature_7' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('9.3');</script><li id='features_get-ms2-spectrum_feature_8' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments <args> <spectra></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('9.4');</script><li id='features_get-ms2-spectrum_feature_9' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run get-ms2-spectrum</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('9.5');</script><li id='features_get-ms2-spectrum_feature_10' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('9.6');</script><li id='features_get-ms2-spectrum_feature_11' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val"><actual_output> should match good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:37</span></div></li> <script type="text/javascript">moveProgressBar('9.7');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_14'><th class="step skipped_param" id="row_14_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_14_1"><div><span class="step param">args</span></div></th><th class="step skipped_param" id="row_14_2"><div><span class="step param">spectra</span></div></th><th class="step skipped_param" id="row_14_3"><div><span class="step param">actual_output</span></div></th><th class="step skipped_param" id="row_14_4"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('9.8');</script><tr class='step' id='row_15'><td class="step passed" id="row_15_0"><div><span class="step param">get_ms2_spectrum</span></div></td><td class="step passed" id="row_15_1"><div><span class="step param">--scan-number 2</span></div></td><td class="step passed" id="row_15_2"><div><span class="step param">test.ms2</span></div></td><td class="step passed" id="row_15_3"><div><span class="step param">stdout</span></div></td><td class="step passed" id="row_15_4"><div><span class="step param">standard_get_ms2_spectrum.out</span></div></td></tr> <script type="text/javascript">moveProgressBar('9.9');</script><tr class='step' id='row_16'><td class="step passed" id="row_16_0"><div><span class="step param">get_ms2_spectrum_stats</span></div></td><td class="step passed" id="row_16_1"><div><span class="step param">--stats T --scan-number 2</span></div></td><td class="step passed" id="row_16_2"><div><span class="step param">test.ms2</span></div></td><td class="step passed" id="row_16_3"><div><span class="step param">stdout</span></div></td><td class="step passed" id="row_16_4"><div><span class="step param">standard_get_ms2_spectrum_stats.out</span></div></td></tr> <script type="text/javascript">moveProgressBar('10.0');</script><tr class='step' id='row_17'><td class="step passed" id="row_17_0"><div><span class="step param">get_ms2_spectrum_without_zlines</span></div></td><td class="step passed" id="row_17_1"><div><span class="step param">--scan-number 2-16</span></div></td><td class="step passed" id="row_17_2"><div><span class="step param">test-no-z1.ms2</span></div></td><td class="step passed" id="row_17_3"><div><span class="step param">stdout</span></div></td><td class="step passed" id="row_17_4"><div><span class="step param">standard_get_ms2_spectrum_without_zlines.out</span></div></td></tr> <script type="text/javascript">moveProgressBar('10.1');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: hardklor</span></h2><p class="narrative">hardklor should identify isotopic distributions from high-resolution mass<br/>spectra<br/></p><div class='scenario outline'><span class="scenario_file">features/hardklor.feature:5</span><h3 id="scenario_8"><span class="keyword">Scenario Outline:</span> <span class="val">User runs hardklor</span></h3><ol><li id='features_hardklor_feature_6' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('10.2');</script><li id='features_hardklor_feature_7' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('10.4');</script><li id='features_hardklor_feature_8' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments --overwrite T <spectra></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('10.5');</script><li id='features_hardklor_feature_9' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run hardklor</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('10.6');</script><li id='features_hardklor_feature_10' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('10.7');</script><li id='features_hardklor_feature_11' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/hardklor.mono.txt should match good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:37</span></div></li> <script type="text/javascript">moveProgressBar('10.8');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_14'><th class="step skipped_param" id="row_14_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_14_1"><div><span class="step param">spectra</span></div></th><th class="step skipped_param" id="row_14_2"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('10.9');</script><tr class='step' id='row_15'><td class="step passed" id="row_15_0"><div><span class="step param">hardklor-default</span></div></td><td class="step passed" id="row_15_1"><div><span class="step param">hardklor.test.ms1</span></div></td><td class="step passed" id="row_15_2"><div><span class="step param">hardklor.mono.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('11.0');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: make-pin</span></h2><p class="narrative">make-pin should, given a set of search results files, generate a pin file for<br/>input to crux percolator<br/></p><div class='scenario outline'><span class="scenario_file">features/make-pin.feature:5</span><h3 id="scenario_9"><span class="keyword">Scenario Outline:</span> <span class="val">User runs make-pin</span></h3><ol><li id='features_make-pin_feature_6' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('11.1');</script><li id='features_make-pin_feature_7' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('11.2');</script><li id='features_make-pin_feature_8' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments --overwrite T --output-file <output_file> <target_input></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('11.3');</script><li id='features_make-pin_feature_9' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run make-pin</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('11.5');</script><li id='features_make-pin_feature_10' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('11.6');</script><li id='features_make-pin_feature_11' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/<output_file> should match good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:37</span></div></li> <script type="text/javascript">moveProgressBar('11.7');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_14'><th class="step skipped_param" id="row_14_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_14_1"><div><span class="step param">output_file</span></div></th><th class="step skipped_param" id="row_14_2"><div><span class="step param">target_input</span></div></th><th class="step skipped_param" id="row_14_3"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('11.8');</script><tr class='step' id='row_15'><td class="step passed" id="row_15_0"><div><span class="step param">make-pin-txt</span></div></td><td class="step passed" id="row_15_1"><div><span class="step param">make-pin_txt.pin</span></div></td><td class="step passed" id="row_15_2"><div><span class="step param">sample2.search.target.txt</span></div></td><td class="step passed" id="row_15_3"><div><span class="step param">make-pin_txt.pin</span></div></td></tr> <script type="text/javascript">moveProgressBar('11.9');</script><tr class='step' id='row_16'><td class="step passed" id="row_16_0"><div><span class="step param">make-pin-pep</span></div></td><td class="step passed" id="row_16_1"><div><span class="step param">make-pin_pep.pin</span></div></td><td class="step passed" id="row_16_2"><div><span class="step param">sample2.search.target.pep.xml</span></div></td><td class="step passed" id="row_16_3"><div><span class="step param">make-pin_pep.pin</span></div></td></tr> <script type="text/javascript">moveProgressBar('12.0');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: predict-peptide-ions</span></h2><p class="narrative">predict-peptide-ions should, given a peptide and a charge state, predict the<br/>m/z values of the resulting fragment ions<br/></p><div class='scenario outline'><span class="scenario_file">features/predict-peptide-ions.feature:5</span><h3 id="scenario_10"><span class="keyword">Scenario Outline:</span> <span class="val">User runs predict-peptide-ions</span></h3><ol><li id='features_predict-peptide-ions_feature_6' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('12.1');</script><li id='features_predict-peptide-ions_feature_7' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('12.2');</script><li id='features_predict-peptide-ions_feature_8' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments <args> <seq> <charge></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('12.3');</script><li id='features_predict-peptide-ions_feature_9' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run predict-peptide-ions</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('12.4');</script><li id='features_predict-peptide-ions_feature_10' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('12.5');</script><li id='features_predict-peptide-ions_feature_11' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">stdout should match good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:37</span></div></li> <script type="text/javascript">moveProgressBar('12.7');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_14'><th class="step skipped_param" id="row_14_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_14_1"><div><span class="step param">args</span></div></th><th class="step skipped_param" id="row_14_2"><div><span class="step param">seq</span></div></th><th class="step skipped_param" id="row_14_3"><div><span class="step param">charge</span></div></th><th class="step skipped_param" id="row_14_4"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('12.8');</script><tr class='step' id='row_15'><td class="step passed" id="row_15_0"><div><span class="step param">predict_ions_no_ops</span></div></td><td class="step passed" id="row_15_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_15_2"><div><span class="step param">IAMASEQ</span></div></td><td class="step passed" id="row_15_3"><div><span class="step param">2</span></div></td><td class="step passed" id="row_15_4"><div><span class="step param">standard_predict_ions_no_ops.out</span></div></td></tr> <script type="text/javascript">moveProgressBar('12.9');</script><tr class='step' id='row_16'><td class="step passed" id="row_16_0"><div><span class="step param">predict_ions_b_h2o</span></div></td><td class="step passed" id="row_16_1"><div><span class="step param">--primary-ions b --precursor-ions T --h2o 1</span></div></td><td class="step passed" id="row_16_2"><div><span class="step param">IAMASEQ</span></div></td><td class="step passed" id="row_16_3"><div><span class="step param">2</span></div></td><td class="step passed" id="row_16_4"><div><span class="step param">standard_predict_ions_b_h2o.out</span></div></td></tr> <script type="text/javascript">moveProgressBar('13.0');</script><tr class='step' id='row_17'><td class="step passed" id="row_17_0"><div><span class="step param">predict_ions_y_nh3</span></div></td><td class="step passed" id="row_17_1"><div><span class="step param">--primary-ions y --nh3 1</span></div></td><td class="step passed" id="row_17_2"><div><span class="step param">IAMASEQ</span></div></td><td class="step passed" id="row_17_3"><div><span class="step param">2</span></div></td><td class="step passed" id="row_17_4"><div><span class="step param">standard_predict_ions_y_nh3.out</span></div></td></tr> <script type="text/javascript">moveProgressBar('13.1');</script><tr class='step' id='row_18'><td class="step passed" id="row_18_0"><div><span class="step param">predict_ions_by_flank_max_z1</span></div></td><td class="step passed" id="row_18_1"><div><span class="step param">--primary-ions by --max-ion-charge 1 --flanking T</span></div></td><td class="step passed" id="row_18_2"><div><span class="step param">IAMASEQ</span></div></td><td class="step passed" id="row_18_3"><div><span class="step param">3</span></div></td><td class="step passed" id="row_18_4"><div><span class="step param">standard_predict_ions_by_flank_max_z1.out</span></div></td></tr> <script type="text/javascript">moveProgressBar('13.2');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: print-processed-spectra</span></h2><p class="narrative">print-processed-spectra should process spectra as for scoring xcorr and print<br/>the results to a file<br/></p><div class='scenario outline'><span class="scenario_file">features/print-processed-spectra.feature:5</span><h3 id="scenario_11"><span class="keyword">Scenario Outline:</span> <span class="val">User runs print-processed-spectra</span></h3><ol><li id='features_print-processed-spectra_feature_6' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('13.3');</script><li id='features_print-processed-spectra_feature_7' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('13.4');</script><li id='features_print-processed-spectra_feature_8' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments <args> <input_spectra> <output_spectra></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('13.5');</script><li id='features_print-processed-spectra_feature_9' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run print-processed-spectra</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('13.6');</script><li id='features_print-processed-spectra_feature_10' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('13.8');</script><li id='features_print-processed-spectra_feature_11' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/<output_spectra> should match good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:37</span></div></li> <script type="text/javascript">moveProgressBar('13.9');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_14'><th class="step skipped_param" id="row_14_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_14_1"><div><span class="step param">args</span></div></th><th class="step skipped_param" id="row_14_2"><div><span class="step param">input_spectra</span></div></th><th class="step skipped_param" id="row_14_3"><div><span class="step param">output_spectra</span></div></th><th class="step skipped_param" id="row_14_4"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('14.0');</script><tr class='step' id='row_15'><td class="step passed" id="row_15_0"><div><span class="step param">print_processed_spectrum</span></div></td><td class="step passed" id="row_15_1"><div><span class="step param">--overwrite T --remove-precursor-tolerance 15</span></div></td><td class="step passed" id="row_15_2"><div><span class="step param">test.ms2</span></div></td><td class="step passed" id="row_15_3"><div><span class="step param">processed-test.ms2</span></div></td><td class="step passed" id="row_15_4"><div><span class="step param">processed-test.ms2</span></div></td></tr> <script type="text/javascript">moveProgressBar('14.1');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: psm-convert</span></h2><p class="narrative">psm-convert should read in a file containing peptide-spectrum matches in one<br/>of the variety of supported formats and output the same PSMs in a different<br/>format<br/></p><div class='scenario outline'><span class="scenario_file">features/psm-convert.feature:6</span><h3 id="scenario_12"><span class="keyword">Scenario Outline:</span> <span class="val">User runs psm-convert</span></h3><ol><li id='features_psm-convert_feature_7' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('14.2');</script><li id='features_psm-convert_feature_8' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('14.3');</script><li id='features_psm-convert_feature_9' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments --overwrite T test_results/<results> <out_format></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('14.4');</script><li id='features_psm-convert_feature_10' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run psm-convert</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('14.5');</script><li id='features_psm-convert_feature_11' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I ignore lines matching the pattern: /^H[ \t]+StartTime.*$/</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:29</span></div></li> <script type="text/javascript">moveProgressBar('14.6');</script><li id='features_psm-convert_feature_12' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I ignore lines matching the pattern: /^<msms_pipeline_analysis .*$/</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:29</span></div></li> <script type="text/javascript">moveProgressBar('14.7');</script><li id='features_psm-convert_feature_13' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I ignore lines matching the pattern: /^<parameter .*$/</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:29</span></div></li> <script type="text/javascript">moveProgressBar('14.8');</script><li id='features_psm-convert_feature_14' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I ignore lines matching the pattern: /^<MzIdentML .*$/</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:29</span></div></li> <script type="text/javascript">moveProgressBar('15.0');</script><li id='features_psm-convert_feature_15' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('15.1');</script><li id='features_psm-convert_feature_16' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/<actual_output> should match good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:37</span></div></li> <script type="text/javascript">moveProgressBar('15.2');</script></ol><div class="examples"><pre class="comment"># Generate results with static-anywhere, variable-anywhere, static-nterm, static-cterm (results1.txt)<br/># tide-search --mods-spec C+57.02,2M+15.99 --nterm-peptide-mods-spec X+1.7 --cterm-peptide-mods-spec X+1.8 demo.ms2 small-yeast.fasta<br/># Generate results with static-anywhere, variable-nterm, variable-cterm (results2.txt)<br/># tide-search --mods-spec C+57.02 --nterm-peptide-mods-spec 1A+1.7 --cterm-peptide-mods-spec 1K+1.8 demo.ms2 small-yeast.fasta<br/></pre><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_25'><th class="step skipped_param" id="row_25_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_25_1"><div><span class="step param">results</span></div></th><th class="step skipped_param" id="row_25_2"><div><span class="step param">out_format</span></div></th><th class="step skipped_param" id="row_25_3"><div><span class="step param">actual_output</span></div></th><th class="step skipped_param" id="row_25_4"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('15.3');</script><tr class='step' id='row_26'><td class="step passed" id="row_26_0"><div><span class="step param">psmconv-txt-to-txt1</span></div></td><td class="step passed" id="row_26_1"><div><span class="step param">results1.txt</span></div></td><td class="step passed" id="row_26_2"><div><span class="step param">tsv</span></div></td><td class="step passed" id="row_26_3"><div><span class="step param">psm-convert.txt</span></div></td><td class="step passed" id="row_26_4"><div><span class="step param">psmconv-from-txt1.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('15.4');</script><tr class='step' id='row_27'><td class="step passed" id="row_27_0"><div><span class="step param">psmconv-txt-to-txt2</span></div></td><td class="step passed" id="row_27_1"><div><span class="step param">results2.txt</span></div></td><td class="step passed" id="row_27_2"><div><span class="step param">tsv</span></div></td><td class="step passed" id="row_27_3"><div><span class="step param">psm-convert.txt</span></div></td><td class="step passed" id="row_27_4"><div><span class="step param">psmconv-from-txt2.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('15.5');</script><tr class='step' id='row_29'><td class="step passed" id="row_29_0"><div><span class="step param">psmconv-txt-to-html1</span></div></td><td class="step passed" id="row_29_1"><div><span class="step param">results1.txt</span></div></td><td class="step passed" id="row_29_2"><div><span class="step param">html</span></div></td><td class="step passed" id="row_29_3"><div><span class="step param">psm-convert.html</span></div></td><td class="step passed" id="row_29_4"><div><span class="step param">psmconv-from-txt1.html</span></div></td></tr> <script type="text/javascript">moveProgressBar('15.6');</script><tr class='step' id='row_30'><td class="step passed" id="row_30_0"><div><span class="step param">psmconv-txt-to-html2</span></div></td><td class="step passed" id="row_30_1"><div><span class="step param">results2.txt</span></div></td><td class="step passed" id="row_30_2"><div><span class="step param">html</span></div></td><td class="step passed" id="row_30_3"><div><span class="step param">psm-convert.html</span></div></td><td class="step passed" id="row_30_4"><div><span class="step param">psmconv-from-txt2.html</span></div></td></tr> <script type="text/javascript">moveProgressBar('15.7');</script><tr class='step' id='row_33'><td class="step passed" id="row_33_0"><div><span class="step param">psmconv-txt-to-pin1</span></div></td><td class="step passed" id="row_33_1"><div><span class="step param">results1.txt</span></div></td><td class="step passed" id="row_33_2"><div><span class="step param">pin</span></div></td><td class="step passed" id="row_33_3"><div><span class="step param">psm-convert.pin</span></div></td><td class="step passed" id="row_33_4"><div><span class="step param">psmconv-from-txt1.pin</span></div></td></tr> <script type="text/javascript">moveProgressBar('15.8');</script><tr class='step' id='row_34'><td class="step passed" id="row_34_0"><div><span class="step param">psmconv-txt-to-pin2</span></div></td><td class="step passed" id="row_34_1"><div><span class="step param">results2.txt</span></div></td><td class="step passed" id="row_34_2"><div><span class="step param">pin</span></div></td><td class="step passed" id="row_34_3"><div><span class="step param">psm-convert.pin</span></div></td><td class="step passed" id="row_34_4"><div><span class="step param">psmconv-from-txt2.pin</span></div></td></tr> <script type="text/javascript">moveProgressBar('15.9');</script><tr class='step' id='row_35'><td class="step passed" id="row_35_0"><div><span class="step param">psmconv-txt-to-pep1</span></div></td><td class="step passed" id="row_35_1"><div><span class="step param">results1.txt</span></div></td><td class="step passed" id="row_35_2"><div><span class="step param">pepxml</span></div></td><td class="step passed" id="row_35_3"><div><span class="step param">psm-convert.pep.xml</span></div></td><td class="step passed" id="row_35_4"><div><span class="step param">psmconv-from-txt1.pep.xml</span></div></td></tr> <script type="text/javascript">moveProgressBar('16.1');</script><tr class='step' id='row_36'><td class="step passed" id="row_36_0"><div><span class="step param">psmconv-txt-to-pep2</span></div></td><td class="step passed" id="row_36_1"><div><span class="step param">results2.txt</span></div></td><td class="step passed" id="row_36_2"><div><span class="step param">pepxml</span></div></td><td class="step passed" id="row_36_3"><div><span class="step param">psm-convert.pep.xml</span></div></td><td class="step passed" id="row_36_4"><div><span class="step param">psmconv-from-txt2.pep.xml</span></div></td></tr> <script type="text/javascript">moveProgressBar('16.2');</script><tr class='step' id='row_37'><td class="step passed" id="row_37_0"><div><span class="step param">psmconv-txt-to-mzid1</span></div></td><td class="step passed" id="row_37_1"><div><span class="step param">results1.txt</span></div></td><td class="step passed" id="row_37_2"><div><span class="step param">mzidentml</span></div></td><td class="step passed" id="row_37_3"><div><span class="step param">psm-convert.mzid</span></div></td><td class="step passed" id="row_37_4"><div><span class="step param">psmconv-from-txt1.mzid</span></div></td></tr> <script type="text/javascript">moveProgressBar('16.3');</script><tr class='step' id='row_38'><td class="step passed" id="row_38_0"><div><span class="step param">psmconv-txt-to-mzid2</span></div></td><td class="step passed" id="row_38_1"><div><span class="step param">results2.txt</span></div></td><td class="step passed" id="row_38_2"><div><span class="step param">mzidentml</span></div></td><td class="step passed" id="row_38_3"><div><span class="step param">psm-convert.mzid</span></div></td><td class="step passed" id="row_38_4"><div><span class="step param">psmconv-from-txt2.mzid</span></div></td></tr> <script type="text/javascript">moveProgressBar('16.4');</script><tr class='step' id='row_42'><td class="step passed" id="row_42_0"><div><span class="step param">psmconv-pep-to-txt1</span></div></td><td class="step passed" id="row_42_1"><div><span class="step param">results1.pep.xml</span></div></td><td class="step passed" id="row_42_2"><div><span class="step param">tsv</span></div></td><td class="step passed" id="row_42_3"><div><span class="step param">psm-convert.txt</span></div></td><td class="step passed" id="row_42_4"><div><span class="step param">psmconv-from-pep1.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('16.5');</script><tr class='step' id='row_43'><td class="step passed" id="row_43_0"><div><span class="step param">psmconv-pep-to-txt2</span></div></td><td class="step passed" id="row_43_1"><div><span class="step param">results2.pep.xml</span></div></td><td class="step passed" id="row_43_2"><div><span class="step param">tsv</span></div></td><td class="step passed" id="row_43_3"><div><span class="step param">psm-convert.txt</span></div></td><td class="step passed" id="row_43_4"><div><span class="step param">psmconv-from-pep2.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('16.6');</script><tr class='step' id='row_44'><td class="step passed" id="row_44_0"><div><span class="step param">psmconv-mzid-to-txt1</span></div></td><td class="step passed" id="row_44_1"><div><span class="step param">results1.mzid</span></div></td><td class="step passed" id="row_44_2"><div><span class="step param">tsv</span></div></td><td class="step passed" id="row_44_3"><div><span class="step param">psm-convert.txt</span></div></td><td class="step passed" id="row_44_4"><div><span class="step param">psmconv-from-mzid1.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('16.7');</script><tr class='step' id='row_45'><td class="step passed" id="row_45_0"><div><span class="step param">psmconv-mzid-to-txt2</span></div></td><td class="step passed" id="row_45_1"><div><span class="step param">results2.mzid</span></div></td><td class="step passed" id="row_45_2"><div><span class="step param">tsv</span></div></td><td class="step passed" id="row_45_3"><div><span class="step param">psm-convert.txt</span></div></td><td class="step passed" id="row_45_4"><div><span class="step param">psmconv-from-mzid2.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('16.8');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: q-ranker</span></h2><p class="narrative">q-ranker should re-rank a collection of PSMs using the Q-ranker algorithm<br/></p><div class='scenario outline'><span class="scenario_file">features/q-ranker.feature:4</span><h3 id="scenario_13"><span class="keyword">Scenario Outline:</span> <span class="val">User runs q-ranker</span></h3><ol><li id='features_q-ranker_feature_5' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('16.9');</script><li id='features_q-ranker_feature_6' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('17.0');</script><li id='features_q-ranker_feature_7' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments <args> <spectra> <search_results></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('17.1');</script><li id='features_q-ranker_feature_8' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run q-ranker</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('17.3');</script><li id='features_q-ranker_feature_9' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('17.4');</script><li id='features_q-ranker_feature_10' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/<actual_output> should match good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:37</span></div></li> <script type="text/javascript">moveProgressBar('17.5');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_13'><th class="step skipped_param" id="row_13_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_13_1"><div><span class="step param">args</span></div></th><th class="step skipped_param" id="row_13_2"><div><span class="step param">spectra</span></div></th><th class="step skipped_param" id="row_13_3"><div><span class="step param">search_results</span></div></th><th class="step skipped_param" id="row_13_4"><div><span class="step param">actual_output</span></div></th><th class="step skipped_param" id="row_13_5"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('17.6');</script><tr class='step' id='row_14'><td class="step passed" id="row_14_0"><div><span class="step param">qranker-separate</span></div></td><td class="step passed" id="row_14_1"><div><span class="step param">--parameter-file params/set_rand_seed_only --separate-searches sample3.search.decoy.txt</span></div></td><td class="step passed" id="row_14_2"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_14_3"><div><span class="step param">sample3.search.target.txt</span></div></td><td class="step passed" id="row_14_4"><div><span class="step param">q-ranker.target.psms.txt</span></div></td><td class="step passed" id="row_14_5"><div><span class="step param">qranker-sep.target.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('17.7');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: search-for-xlinks</span></h2><p class="narrative">search-for-xlinks should search a collection of spectra against a sequence<br/>database, returning a collection of matches corresponding to linear and<br/>cross-linked peptides scored by XCorr<br/></p><div class='scenario outline'><span class="scenario_file">features/search-for-xlinks.feature:6</span><h3 id="scenario_14"><span class="keyword">Scenario Outline:</span> <span class="val">User runs search-for-xlinks</span></h3><ol><li id='features_search-for-xlinks_feature_7' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('17.8');</script><li id='features_search-for-xlinks_feature_8' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('17.9');</script><li id='features_search-for-xlinks_feature_9' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments <args> <spectra> <fasta> <sites> <mass></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('18.0');</script><li id='features_search-for-xlinks_feature_10' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run search-for-xlinks</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('18.1');</script><li id='features_search-for-xlinks_feature_11' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('18.2');</script><li id='features_search-for-xlinks_feature_12' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/<actual_output> should match good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:37</span></div></li> <script type="text/javascript">moveProgressBar('18.4');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_15'><th class="step skipped_param" id="row_15_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_15_1"><div><span class="step param">args</span></div></th><th class="step skipped_param" id="row_15_2"><div><span class="step param">spectra</span></div></th><th class="step skipped_param" id="row_15_3"><div><span class="step param">fasta</span></div></th><th class="step skipped_param" id="row_15_4"><div><span class="step param">sites</span></div></th><th class="step skipped_param" id="row_15_5"><div><span class="step param">mass</span></div></th><th class="step skipped_param" id="row_15_6"><div><span class="step param">actual_output</span></div></th><th class="step skipped_param" id="row_15_7"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('18.5');</script><tr class='step' id='row_16'><td class="step passed" id="row_16_0"><div><span class="step param">xlink-db</span></div></td><td class="step passed" id="row_16_1"><div><span class="step param">--parameter-file params/xlink.db</span></div></td><td class="step passed" id="row_16_2"><div><span class="step param">xlink.ms2</span></div></td><td class="step passed" id="row_16_3"><div><span class="step param">xlink.db.fasta</span></div></td><td class="step passed" id="row_16_4"><div><span class="step param">K:K</span></div></td><td class="step passed" id="row_16_5"><div><span class="step param">222</span></div></td><td class="step passed" id="row_16_6"><div><span class="step param">xlink_peptides.txt</span></div></td><td class="step passed" id="row_16_7"><div><span class="step param">xlink_peptides.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('18.6');</script><tr class='step' id='row_17'><td class="step passed" id="row_17_0"><div><span class="step param">search-for-xlinks</span></div></td><td class="step passed" id="row_17_1"><div><span class="step param">--parameter-file params/xlink</span></div></td><td class="step passed" id="row_17_2"><div><span class="step param">xlink.ms2</span></div></td><td class="step passed" id="row_17_3"><div><span class="step param">xlink.fasta</span></div></td><td class="step passed" id="row_17_4"><div><span class="step param">E:K,D:K</span></div></td><td class="step passed" id="row_17_5"><div><span class="step param">-18.01</span></div></td><td class="step passed" id="row_17_6"><div><span class="step param">search-for-xlinks.target.txt</span></div></td><td class="step passed" id="row_17_7"><div><span class="step param">search-xlink.target.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('18.7');</script><tr class='step' id='row_18'><td class="step passed" id="row_18_0"><div><span class="step param">search-for-xlinks-cz-ions</span></div></td><td class="step passed" id="row_18_1"><div><span class="step param">--parameter-file params/xlink-cz</span></div></td><td class="step passed" id="row_18_2"><div><span class="step param">xlink.ms2</span></div></td><td class="step passed" id="row_18_3"><div><span class="step param">xlink.fasta</span></div></td><td class="step passed" id="row_18_4"><div><span class="step param">E:K,D:K</span></div></td><td class="step passed" id="row_18_5"><div><span class="step param">-18.01</span></div></td><td class="step passed" id="row_18_6"><div><span class="step param">search-for-xlinks.target.txt</span></div></td><td class="step passed" id="row_18_7"><div><span class="step param">search-for-xlinks.cz.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('18.8');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: spectral-counts</span></h2><p class="narrative">spectral-counts should quantify peptides or proteins using one of three<br/>spectral counting methods<br/></p><div class='scenario outline'><span class="scenario_file">features/spectral-counts.feature:5</span><h3 id="scenario_15"><span class="keyword">Scenario Outline:</span> <span class="val">User runs spectral-counts</span></h3><ol><li id='features_spectral-counts_feature_6' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('18.9');</script><li id='features_spectral-counts_feature_7' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('19.0');</script><li id='features_spectral-counts_feature_8' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments --overwrite T <args> <results></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('19.1');</script><li id='features_spectral-counts_feature_9' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run spectral-counts</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('19.2');</script><li id='features_spectral-counts_feature_10' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('19.3');</script><li id='features_spectral-counts_feature_11' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/spectral-counts.target.txt should match good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:37</span></div></li> <script type="text/javascript">moveProgressBar('19.4');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_14'><th class="step skipped_param" id="row_14_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_14_1"><div><span class="step param">args</span></div></th><th class="step skipped_param" id="row_14_2"><div><span class="step param">results</span></div></th><th class="step skipped_param" id="row_14_3"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('19.6');</script><tr class='step' id='row_15'><td class="step passed" id="row_15_0"><div><span class="step param">spectral-counts-raw</span></div></td><td class="step passed" id="row_15_1"><div><span class="step param">--parameter-file params/raw --protein-database test.fasta</span></div></td><td class="step passed" id="row_15_2"><div><span class="step param">test.target.txt</span></div></td><td class="step passed" id="row_15_3"><div><span class="step param">spectral-counts.raw.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('19.7');</script><tr class='step' id='row_16'><td class="step passed" id="row_16_0"><div><span class="step param">spectral-counts-sin</span></div></td><td class="step passed" id="row_16_1"><div><span class="step param">--parameter-file params/sin --protein-database test.fasta</span></div></td><td class="step passed" id="row_16_2"><div><span class="step param">test.target.txt</span></div></td><td class="step passed" id="row_16_3"><div><span class="step param">spectral-counts.sin.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('19.8');</script><tr class='step' id='row_17'><td class="step passed" id="row_17_0"><div><span class="step param">spectral-counts-nsaf</span></div></td><td class="step passed" id="row_17_1"><div><span class="step param">--parameter-file params/nsaf --protein-database test.fasta</span></div></td><td class="step passed" id="row_17_2"><div><span class="step param">test.target.txt</span></div></td><td class="step passed" id="row_17_3"><div><span class="step param">spectral-counts.nsaf.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('19.9');</script><tr class='step' id='row_18'><td class="step passed" id="row_18_0"><div><span class="step param">spectral-counts-empai</span></div></td><td class="step passed" id="row_18_1"><div><span class="step param">--parameter-file params/empai --protein-database test.fasta</span></div></td><td class="step passed" id="row_18_2"><div><span class="step param">test.target.txt</span></div></td><td class="step passed" id="row_18_3"><div><span class="step param">spectral-counts.empai.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('20.0');</script><tr class='step' id='row_19'><td class="step passed" id="row_19_0"><div><span class="step param">spectral-counts-dnsaf</span></div></td><td class="step passed" id="row_19_1"><div><span class="step param">--parameter-file params/dnsaf --protein-database test.fasta</span></div></td><td class="step passed" id="row_19_2"><div><span class="step param">test.target.txt</span></div></td><td class="step passed" id="row_19_3"><div><span class="step param">spectral-counts.dnsaf.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('20.1');</script><tr class='step' id='row_20'><td class="step passed" id="row_20_0"><div><span class="step param">spectral-counts-pepxml</span></div></td><td class="step passed" id="row_20_1"><div><span class="step param">--parameter-file params/nsaf --protein-database small-yeast.fasta</span></div></td><td class="step passed" id="row_20_2"><div><span class="step param">sample.target.pep.xml</span></div></td><td class="step passed" id="row_20_3"><div><span class="step param">spectral-counts.pepxml.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('20.2');</script><tr class='step' id='row_21'><td class="step passed" id="row_21_0"><div><span class="step param">spectral-counts-custom</span></div></td><td class="step passed" id="row_21_1"><div><span class="step param">--parameter-file params/spc-custom --protein-database small-yeast.fasta</span></div></td><td class="step passed" id="row_21_2"><div><span class="step param">sample.target.pep.xml</span></div></td><td class="step passed" id="row_21_3"><div><span class="step param">spectral-counts.pepxml.custom.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('20.3');</script><tr class='step' id='row_22'><td class="step passed" id="row_22_0"><div><span class="step param">spectral-counts-simple</span></div></td><td class="step passed" id="row_22_1"><div><span class="step param">--parameter-file params/spc-simple --protein-database small-yeast.fasta</span></div></td><td class="step passed" id="row_22_2"><div><span class="step param">sample.target.pep.xml</span></div></td><td class="step passed" id="row_22_3"><div><span class="step param">spectral-counts.simple.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('20.4');</script><tr class='step' id='row_23'><td class="step passed" id="row_23_0"><div><span class="step param">spectral-counts-none</span></div></td><td class="step passed" id="row_23_1"><div><span class="step param">--parameter-file params/spc-none --protein-database small-yeast.fasta</span></div></td><td class="step passed" id="row_23_2"><div><span class="step param">sample.target.pep.xml</span></div></td><td class="step passed" id="row_23_3"><div><span class="step param">spectral-counts.none.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('20.5');</script><tr class='step' id='row_24'><td class="step passed" id="row_24_0"><div><span class="step param">spectral-counts-peptideprophet</span></div></td><td class="step passed" id="row_24_1"><div><span class="step param">--parameter-file params/spc-pp --protein-database small-yeast.fasta</span></div></td><td class="step passed" id="row_24_2"><div><span class="step param">sample.target.pep.xml</span></div></td><td class="step passed" id="row_24_3"><div><span class="step param">spectral-counts.peptideprophet.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('20.7');</script><tr class='step' id='row_25'><td class="step passed" id="row_25_0"><div><span class="step param">spectral-counts-pepxml-nodb</span></div></td><td class="step passed" id="row_25_1"><div><span class="step param">--parameter-file params/raw</span></div></td><td class="step passed" id="row_25_2"><div><span class="step param">sample.target.pep.xml</span></div></td><td class="step passed" id="row_25_3"><div><span class="step param">spectral-counts.pepxml.nodb.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('20.8');</script><tr class='step' id='row_26'><td class="step passed" id="row_26_0"><div><span class="step param">spectral-counts-tsv-nodb</span></div></td><td class="step passed" id="row_26_1"><div><span class="step param">--parameter-file params/raw</span></div></td><td class="step passed" id="row_26_2"><div><span class="step param">sample.target.psms.txt</span></div></td><td class="step passed" id="row_26_3"><div><span class="step param">spectral-counts.raw.nodb.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('20.9');</script><tr class='step' id='row_28'><td class="step passed" id="row_28_0"><div><span class="step param">spectral-counts-barista</span></div></td><td class="step passed" id="row_28_1"><div><span class="step param">--parameter-file params/nsaf --protein-database small-yeast.fasta</span></div></td><td class="step passed" id="row_28_2"><div><span class="step param">sample2.target.psms.txt</span></div></td><td class="step passed" id="row_28_3"><div><span class="step param">spectral-counts.barista.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('21.0');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: tide-index</span></h2><p class="narrative">tide-index should create an index for all peptides in a fasta file, for use in<br/>subsequent calls to tide-search<br/></p><div class='scenario outline'><span class="scenario_file">features/tide-index.feature:5</span><h3 id="scenario_16"><span class="keyword">Scenario Outline:</span> <span class="val">User runs tide-index / tide-search</span></h3><ol><li id='features_tide-index_feature_6' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('21.1');</script><li id='features_tide-index_feature_7' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('21.2');</script><li id='features_tide-index_feature_8' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments --overwrite T --peptide-list T <index_args> <fasta> <index></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('21.3');</script><li id='features_tide-index_feature_9' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run tide-index</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('21.4');</script><li id='features_tide-index_feature_10' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('21.5');</script><li id='features_tide-index_feature_11' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/<actual_targets> should contain the same lines as good_results/<expected_targets></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:41</span></div></li> <script type="text/javascript">moveProgressBar('21.6');</script><li id='features_tide-index_feature_12' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/<actual_decoys> should contain the same lines as good_results/<expected_decoys></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:41</span></div></li> <script type="text/javascript">moveProgressBar('21.7');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_15'><th class="step skipped_param" id="row_15_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_15_1"><div><span class="step param">index_args</span></div></th><th class="step skipped_param" id="row_15_2"><div><span class="step param">fasta</span></div></th><th class="step skipped_param" id="row_15_3"><div><span class="step param">index</span></div></th><th class="step skipped_param" id="row_15_4"><div><span class="step param">actual_targets</span></div></th><th class="step skipped_param" id="row_15_5"><div><span class="step param">expected_targets</span></div></th><th class="step skipped_param" id="row_15_6"><div><span class="step param">actual_decoys</span></div></th><th class="step skipped_param" id="row_15_7"><div><span class="step param">expected_decoys</span></div></th></tr> <script type="text/javascript">moveProgressBar('21.9');</script><tr class='step' id='row_16'><td class="step passed" id="row_16_0"><div><span class="step param">tide-default</span></div></td><td class="step passed" id="row_16_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_16_2"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_16_3"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_16_4"><div><span class="step param">tide-index.peptides.target.txt</span></div></td><td class="step passed" id="row_16_5"><div><span class="step param">tide-default.target.txt</span></div></td><td class="step passed" id="row_16_6"><div><span class="step param">tide-index.peptides.decoy.txt</span></div></td><td class="step passed" id="row_16_7"><div><span class="step param">tide-default.decoy.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('22.0');</script><tr class='step' id='row_17'><td class="step passed" id="row_17_0"><div><span class="step param">tide-dups</span></div></td><td class="step passed" id="row_17_1"><div><span class="step param">--allow-dups T</span></div></td><td class="step passed" id="row_17_2"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_17_3"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_17_4"><div><span class="step param">tide-index.peptides.target.txt</span></div></td><td class="step passed" id="row_17_5"><div><span class="step param">tide-dups.target.txt</span></div></td><td class="step passed" id="row_17_6"><div><span class="step param">tide-index.peptides.decoy.txt</span></div></td><td class="step passed" id="row_17_7"><div><span class="step param">tide-dups.decoy.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('22.1');</script><tr class='step' id='row_18'><td class="step passed" id="row_18_0"><div><span class="step param">tide-proteinReverse</span></div></td><td class="step passed" id="row_18_1"><div><span class="step param">--decoy-format PROTEIN-REVERSE</span></div></td><td class="step passed" id="row_18_2"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_18_3"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_18_4"><div><span class="step param">tide-index.peptides.target.txt</span></div></td><td class="step passed" id="row_18_5"><div><span class="step param">tide-reverse.target.txt</span></div></td><td class="step passed" id="row_18_6"><div><span class="step param">tide-index.peptides.decoy.txt</span></div></td><td class="step passed" id="row_18_7"><div><span class="step param">tide-reverse.decoy.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('22.2');</script><tr class='step' id='row_19'><td class="step passed" id="row_19_0"><div><span class="step param">tide-temp-dir</span></div></td><td class="step passed" id="row_19_1"><div><span class="step param">--temp-dir .</span></div></td><td class="step passed" id="row_19_2"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_19_3"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_19_4"><div><span class="step param">tide-index.peptides.target.txt</span></div></td><td class="step passed" id="row_19_5"><div><span class="step param">tide-default.target.txt</span></div></td><td class="step passed" id="row_19_6"><div><span class="step param">tide-index.peptides.decoy.txt</span></div></td><td class="step passed" id="row_19_7"><div><span class="step param">tide-default.decoy.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('22.3');</script><tr class='step' id='row_20'><td class="step passed" id="row_20_0"><div><span class="step param">tide-no-enzyme</span></div></td><td class="step passed" id="row_20_1"><div><span class="step param">--enzyme no-enzyme</span></div></td><td class="step passed" id="row_20_2"><div><span class="step param">test.fasta</span></div></td><td class="step passed" id="row_20_3"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_20_4"><div><span class="step param">tide-index.peptides.target.txt</span></div></td><td class="step passed" id="row_20_5"><div><span class="step param">tide-no-enzyme.target.txt</span></div></td><td class="step passed" id="row_20_6"><div><span class="step param">tide-index.peptides.decoy.txt</span></div></td><td class="step passed" id="row_20_7"><div><span class="step param">tide-no-enzyme.decoy.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('22.4');</script></table></div></div></div><div class="feature"><h2><span class="val">Feature: tide-index / tide-search</span></h2><p class="narrative">tide-index should create an index for all peptides in a fasta file, for use in<br/>subsequent calls to tide-search<br/>tide-search should search a collection of spectra against a sequence database,<br/>returning a collection of peptide-spectrum matches (PSMs)<br/></p><div class='scenario outline'><span class="scenario_file">features/tide-search.feature:7</span><h3 id="scenario_17"><span class="keyword">Scenario Outline:</span> <span class="val">User runs tide-index / tide-search</span></h3><ol><li id='features_tide-search_feature_8' class='step skipped'><div class="step_name"><span class="keyword">Given </span><span class="step val">the path to Crux is ../../src/crux</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:8</span></div></li> <script type="text/javascript">moveProgressBar('22.5');</script><li id='features_tide-search_feature_9' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I want to run a test named <test_name></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:12</span></div></li> <script type="text/javascript">moveProgressBar('22.6');</script><li id='features_tide-search_feature_10' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments --overwrite T --seed 7 <index_args> <fasta> <index></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('22.7');</script><li id='features_tide-search_feature_11' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run tide-index as an intermediate step</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:25</span></div></li> <script type="text/javascript">moveProgressBar('22.8');</script><li id='features_tide-search_feature_12' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('23.0');</script><li id='features_tide-search_feature_13' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">I pass the arguments --overwrite T --file-column F <search_args> <spectra> <index></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:16</span></div></li> <script type="text/javascript">moveProgressBar('23.1');</script><li id='features_tide-search_feature_14' class='step skipped'><div class="step_name"><span class="keyword">When </span><span class="step val">I run tide-search</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:20</span></div></li> <script type="text/javascript">moveProgressBar('23.2');</script><li id='features_tide-search_feature_15' class='step skipped'><div class="step_name"><span class="keyword">Then </span><span class="step val">the return value should be 0</span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:33</span></div></li> <script type="text/javascript">moveProgressBar('23.3');</script><li id='features_tide-search_feature_16' class='step skipped'><div class="step_name"><span class="keyword">And </span><span class="step val">crux-output/<actual_output> should contain the same lines as good_results/<expected_output></span></div><div class="step_file"><span>features/step_definitions/SmokeTestStepDefinitions.rb:41</span></div></li> <script type="text/javascript">moveProgressBar('23.4');</script></ol><div class="examples"><h4><span class="keyword">Examples</span> <span class="val"></span></h4><table><tr class='step' id='row_19'><th class="step skipped_param" id="row_19_0"><div><span class="step param">test_name</span></div></th><th class="step skipped_param" id="row_19_1"><div><span class="step param">index_args</span></div></th><th class="step skipped_param" id="row_19_2"><div><span class="step param">search_args</span></div></th><th class="step skipped_param" id="row_19_3"><div><span class="step param">fasta</span></div></th><th class="step skipped_param" id="row_19_4"><div><span class="step param">index</span></div></th><th class="step skipped_param" id="row_19_5"><div><span class="step param">spectra</span></div></th><th class="step skipped_param" id="row_19_6"><div><span class="step param">actual_output</span></div></th><th class="step skipped_param" id="row_19_7"><div><span class="step param">expected_output</span></div></th></tr> <script type="text/javascript">moveProgressBar('23.5');</script><tr class='step' id='row_20'><td class="step passed" id="row_20_0"><div><span class="step param">tide-default</span></div></td><td class="step passed" id="row_20_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_20_2"><div><span class="step param"></span></div></td><td class="step passed" id="row_20_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_20_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_20_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_20_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_20_7"><div><span class="step param">tide-default.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('23.6');</script><tr class='step' id='row_22'><td class="step passed" id="row_22_0"><div><span class="step param">tide-peplen</span></div></td><td class="step passed" id="row_22_1"><div><span class="step param">--min-length 5 --max-length 10</span></div></td><td class="step passed" id="row_22_2"><div><span class="step param"></span></div></td><td class="step passed" id="row_22_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_22_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_22_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_22_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_22_7"><div><span class="step param">tide-peplen.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('23.7');</script><tr class='step' id='row_23'><td class="step passed" id="row_23_0"><div><span class="step param">tide-pepmass</span></div></td><td class="step passed" id="row_23_1"><div><span class="step param">--min-mass 1000 --max-mass 2000</span></div></td><td class="step passed" id="row_23_2"><div><span class="step param"></span></div></td><td class="step passed" id="row_23_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_23_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_23_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_23_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_23_7"><div><span class="step param">tide-pepmass.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('23.8');</script><tr class='step' id='row_24'><td class="step passed" id="row_24_0"><div><span class="step param">tide-avgmass</span></div></td><td class="step passed" id="row_24_1"><div><span class="step param">--isotopic-mass average</span></div></td><td class="step passed" id="row_24_2"><div><span class="step param"></span></div></td><td class="step passed" id="row_24_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_24_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_24_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_24_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_24_7"><div><span class="step param">tide-avgmass.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('23.9');</script><tr class='step' id='row_25'><td class="step passed" id="row_25_0"><div><span class="step param">tide-clipn</span></div></td><td class="step passed" id="row_25_1"><div><span class="step param">--clip-nterm-methionine T</span></div></td><td class="step passed" id="row_25_2"><div><span class="step param"></span></div></td><td class="step passed" id="row_25_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_25_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_25_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_25_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_25_7"><div><span class="step param">tide-clipn.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('24.0');</script><tr class='step' id='row_26'><td class="step passed" id="row_26_0"><div><span class="step param">tide-mods1</span></div></td><td class="step passed" id="row_26_1"><div><span class="step param">--mods-spec C+57.02146,2M+15.9949,1STY+79.966331</span></div></td><td class="step passed" id="row_26_2"><div><span class="step param"></span></div></td><td class="step passed" id="row_26_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_26_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_26_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_26_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_26_7"><div><span class="step param">tide-mods1.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('24.2');</script><tr class='step' id='row_27'><td class="step passed" id="row_27_0"><div><span class="step param">tide-mods1limit</span></div></td><td class="step passed" id="row_27_1"><div><span class="step param">--mods-spec C+57.02146,2M+15.9949,1STY+79.966331 --max-mods 1</span></div></td><td class="step passed" id="row_27_2"><div><span class="step param"></span></div></td><td class="step passed" id="row_27_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_27_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_27_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_27_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_27_7"><div><span class="step param">tide-mods1limit.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('24.3');</script><tr class='step' id='row_28'><td class="step passed" id="row_28_0"><div><span class="step param">tide-mods1min</span></div></td><td class="step passed" id="row_28_1"><div><span class="step param">--mods-spec C+57.02146,2M+15.9949,1STY+79.966331 --min-mods 1</span></div></td><td class="step passed" id="row_28_2"><div><span class="step param"></span></div></td><td class="step passed" id="row_28_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_28_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_28_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_28_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_28_7"><div><span class="step param">tide-mods1min.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('24.4');</script><tr class='step' id='row_29'><td class="step passed" id="row_29_0"><div><span class="step param">tide-modsn</span></div></td><td class="step passed" id="row_29_1"><div><span class="step param">--nterm-peptide-mods-spec 1E-18.0106,C-17.0265</span></div></td><td class="step passed" id="row_29_2"><div><span class="step param"></span></div></td><td class="step passed" id="row_29_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_29_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_29_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_29_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_29_7"><div><span class="step param">tide-modsn.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('24.5');</script><tr class='step' id='row_30'><td class="step passed" id="row_30_0"><div><span class="step param">tide-modsc</span></div></td><td class="step passed" id="row_30_1"><div><span class="step param">--cterm-peptide-mods-spec X+21.9819</span></div></td><td class="step passed" id="row_30_2"><div><span class="step param"></span></div></td><td class="step passed" id="row_30_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_30_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_30_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_30_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_30_7"><div><span class="step param">tide-modsc.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('24.6');</script><tr class='step' id='row_31'><td class="step passed" id="row_31_0"><div><span class="step param">tide-chymo</span></div></td><td class="step passed" id="row_31_1"><div><span class="step param">--enzyme chymotrypsin</span></div></td><td class="step passed" id="row_31_2"><div><span class="step param"></span></div></td><td class="step passed" id="row_31_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_31_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_31_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_31_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_31_7"><div><span class="step param">tide-chymo.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('24.7');</script><tr class='step' id='row_32'><td class="step passed" id="row_32_0"><div><span class="step param">tide-partial</span></div></td><td class="step passed" id="row_32_1"><div><span class="step param">--digestion partial-digest</span></div></td><td class="step passed" id="row_32_2"><div><span class="step param"></span></div></td><td class="step passed" id="row_32_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_32_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_32_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_32_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_32_7"><div><span class="step param">tide-partial.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('24.8');</script><tr class='step' id='row_33'><td class="step passed" id="row_33_0"><div><span class="step param">tide-misscleave</span></div></td><td class="step passed" id="row_33_1"><div><span class="step param">--missed-cleavages 2</span></div></td><td class="step passed" id="row_33_2"><div><span class="step param"></span></div></td><td class="step passed" id="row_33_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_33_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_33_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_33_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_33_7"><div><span class="step param">tide-misscleave.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('24.9');</script><tr class='step' id='row_34'><td class="step passed" id="row_34_0"><div><span class="step param">tide-reverse</span></div></td><td class="step passed" id="row_34_1"><div><span class="step param">--decoy-format peptide-reverse</span></div></td><td class="step passed" id="row_34_2"><div><span class="step param"></span></div></td><td class="step passed" id="row_34_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_34_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_34_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_34_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_34_7"><div><span class="step param">tide-reverse.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('25.0');</script><tr class='step' id='row_37'><td class="step passed" id="row_37_0"><div><span class="step param">tide-masswin</span></div></td><td class="step passed" id="row_37_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_37_2"><div><span class="step param">--precursor-window 5 --precursor-window-type mass</span></div></td><td class="step passed" id="row_37_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_37_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_37_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_37_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_37_7"><div><span class="step param">tide-masswin.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('25.1');</script><tr class='step' id='row_38'><td class="step passed" id="row_38_0"><div><span class="step param">tide-mzwin</span></div></td><td class="step passed" id="row_38_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_38_2"><div><span class="step param">--precursor-window 5 --precursor-window-type mz</span></div></td><td class="step passed" id="row_38_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_38_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_38_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_38_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_38_7"><div><span class="step param">tide-mzwin.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('25.3');</script><tr class='step' id='row_39'><td class="step passed" id="row_39_0"><div><span class="step param">tide-ppmwin</span></div></td><td class="step passed" id="row_39_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_39_2"><div><span class="step param">--precursor-window 5 --precursor-window-type ppm</span></div></td><td class="step passed" id="row_39_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_39_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_39_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_39_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_39_7"><div><span class="step param">tide-ppmwin.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('25.4');</script><tr class='step' id='row_40'><td class="step passed" id="row_40_0"><div><span class="step param">tide-computesp</span></div></td><td class="step passed" id="row_40_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_40_2"><div><span class="step param">--compute-sp T</span></div></td><td class="step passed" id="row_40_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_40_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_40_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_40_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_40_7"><div><span class="step param">tide-computesp.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('25.5');</script><tr class='step' id='row_41'><td class="step passed" id="row_41_0"><div><span class="step param">tide-specmz</span></div></td><td class="step passed" id="row_41_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_41_2"><div><span class="step param">--spectrum-min-mz 800 --spectrum-max-mz 900</span></div></td><td class="step passed" id="row_41_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_41_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_41_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_41_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_41_7"><div><span class="step param">tide-specmz.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('25.6');</script><tr class='step' id='row_42'><td class="step passed" id="row_42_0"><div><span class="step param">tide-minpeaks</span></div></td><td class="step passed" id="row_42_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_42_2"><div><span class="step param">--min-peaks 100</span></div></td><td class="step passed" id="row_42_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_42_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_42_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_42_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_42_7"><div><span class="step param">tide-minpeaks.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('25.7');</script><tr class='step' id='row_43'><td class="step passed" id="row_43_0"><div><span class="step param">tide-speccharge</span></div></td><td class="step passed" id="row_43_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_43_2"><div><span class="step param">--spectrum-charge 3</span></div></td><td class="step passed" id="row_43_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_43_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_43_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_43_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_43_7"><div><span class="step param">tide-speccharge.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('25.8');</script><tr class='step' id='row_44'><td class="step passed" id="row_44_0"><div><span class="step param">tide-scannums</span></div></td><td class="step passed" id="row_44_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_44_2"><div><span class="step param">--scan-number 30-36</span></div></td><td class="step passed" id="row_44_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_44_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_44_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_44_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_44_7"><div><span class="step param">tide-scannums.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('25.9');</script><tr class='step' id='row_45'><td class="step passed" id="row_45_0"><div><span class="step param">tide-rempeaks</span></div></td><td class="step passed" id="row_45_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_45_2"><div><span class="step param">--remove-precursor-peak T --remove-precursor-tolerance 3</span></div></td><td class="step passed" id="row_45_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_45_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_45_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_45_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_45_7"><div><span class="step param">tide-rempeaks.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('26.0');</script><tr class='step' id='row_46'><td class="step passed" id="row_46_0"><div><span class="step param">tide-useflank</span></div></td><td class="step passed" id="row_46_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_46_2"><div><span class="step param">--use-flanking-peaks T</span></div></td><td class="step passed" id="row_46_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_46_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_46_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_46_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_46_7"><div><span class="step param">tide-useflank.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('26.1');</script><tr class='step' id='row_47'><td class="step passed" id="row_47_0"><div><span class="step param">tide-usenl</span></div></td><td class="step passed" id="row_47_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_47_2"><div><span class="step param">--use-neutral-loss-peaks T</span></div></td><td class="step passed" id="row_47_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_47_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" 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class="step passed" id="row_49_7"><div><span class="step param">tide-exact-pval.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('26.5');</script><tr class='step' id='row_50'><td class="step passed" id="row_50_0"><div><span class="step param">tide-1thread</span></div></td><td class="step passed" id="row_50_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_50_2"><div><span class="step param">--num-threads 1</span></div></td><td class="step passed" id="row_50_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_50_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_50_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_50_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_50_7"><div><span class="step param">tide-default.txt</span></div></td></tr> 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param">tide-exact-pval-7thread</span></div></td><td class="step passed" id="row_53_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_53_2"><div><span class="step param">--exact-p-value T --num-threads 7</span></div></td><td class="step passed" id="row_53_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_53_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_53_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_53_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_53_7"><div><span class="step param">tide-exact-pval.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('26.9');</script><tr class='step' id='row_54'><td class="step passed" id="row_54_0"><div><span class="step param">tide-concat</span></div></td><td class="step passed" id="row_54_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_54_2"><div><span class="step param">--concat T</span></div></td><td class="step passed" id="row_54_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_54_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_54_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_54_6"><div><span class="step param">tide-search.txt</span></div></td><td class="step passed" id="row_54_7"><div><span class="step param">tide-concat.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('27.0');</script><tr class='step' id='row_55'><td class="step passed" id="row_55_0"><div><span class="step param">tide-isoerr</span></div></td><td class="step passed" id="row_55_1"><div><span class="step param"></span></div></td><td class="step passed" id="row_55_2"><div><span class="step 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id="row_56_3"><div><span class="step param">small-yeast.fasta</span></div></td><td class="step passed" id="row_56_4"><div><span class="step param">tide_test_index</span></div></td><td class="step passed" id="row_56_5"><div><span class="step param">demo.ms2</span></div></td><td class="step passed" id="row_56_6"><div><span class="step param">tide-search.target.txt</span></div></td><td class="step passed" id="row_56_7"><div><span class="step param">tide-isoerrpval.txt</span></div></td></tr> <script type="text/javascript">moveProgressBar('27.2');</script></table></div></div></div><script type="text/javascript">document.getElementById('duration').innerHTML = "Finished in <strong>4m35.144s seconds</strong>";</script><script type="text/javascript">document.getElementById('totals').innerHTML = "116 scenarios (116 passed)<br />913 steps (913 passed)";</script></div></body></html>