From 2075ddc3353c3a2a54fd07eddb94d2c398c04fc9 Mon Sep 17 00:00:00 2001
From: rlibouban <romane.libouban@irisa.fr>
Date: Fri, 22 Sep 2023 14:33:36 +0200
Subject: [PATCH] Change test 1

---
 tools/helixer/helixer.xml | 10 +++-------
 tools/helixer/macros.xml  |  5 ++---
 2 files changed, 5 insertions(+), 10 deletions(-)

diff --git a/tools/helixer/helixer.xml b/tools/helixer/helixer.xml
index d8e893f..1d35dcd 100644
--- a/tools/helixer/helixer.xml
+++ b/tools/helixer/helixer.xml
@@ -11,10 +11,7 @@
 
     <command detect_errors="exit_code"><![CDATA[
 
-        /usr/local/bin/fetch_helixer_models.py
-
-        &&
-    
+        /usr/local/bin/fetch_helixer_models.py &&
         Helixer.py
         --fasta-path '$input'
         --species '$species'
@@ -67,7 +64,7 @@
             </sanitizer>
             <validator type="regex">[0-9a-zA-Z_]+</validator>
         </param>
-        <param name="size" argument="--batch-size" type="integer" value="8" label="Batch size" help="It may then be necessary to reduce it if the GPU runs out of memory" />
+        <param name="size" argument="--batch-size" type="integer" value="8" label="Batch size" help="It may be necessary to reduce it if the GPU runs out of memory" />
         <section name="post_processing" title="Post-processing">
             <param argument="--window-size" type="integer" min="0" value="100" label="Window size" help="This determines the number of bases averaged during the sliding window approach"/>
             <param argument="--edge-threshold" type="float" min="0" max="1" value="0.1" label="Edge threshold" help="This threshold specifies the genic score which defines the start / end boundaries of each candidate region"/>
@@ -81,7 +78,6 @@
         </data>
     </outputs>
     <tests>
-        <!-- Test for land_plant -->
         <test expect_num_outputs="1">
             <!-- Test for species and land_plant-->
             <param name="input" value="sequence.fasta"/>
@@ -90,7 +86,7 @@
                 <param name="lineages" value="land_plant"/>
             </conditional>
             <param name="size" value="8"/>
-            <output name="output" value="ouput_species.gff3" ftype="gff3" lines_diff="3"/>
+            <output name="output" value="ouput_species.gff3" ftype="gff3" compare="sim_size" delta="100"/>
         </test>
         <test expect_num_outputs="1">
             <!-- Test for vertebrates-->
diff --git a/tools/helixer/macros.xml b/tools/helixer/macros.xml
index 65ded99..3d793b9 100644
--- a/tools/helixer/macros.xml
+++ b/tools/helixer/macros.xml
@@ -9,9 +9,9 @@
     </xml>
 
     <xml name="requirements">
-        <container type="docker">gglyptodon/helixer-docker:helixer_v0.3.2_cuda_11.8.0-cudnn8</container>
+        <container type="docker">gglyptodon/helixer-docker:helixer_v@TOOL_VERSION@_cuda_11.8.0-cudnn8</container>
     </xml>
-
+    
     <xml name="subseq" tokens="length,offset,offsetlen">
         <param argument="--subsequence-length" type="integer" min="0" max="213840" value="@LENGTH@" label="Subsequence length: how much of the genome the Neural Network can see at once" help="Should ideally be comfortably longer than the typical gene. For genomes with large genes (>20kpb) it is recommended to increase this parameter."></param>
         <conditional name="option_overlap">
@@ -26,6 +26,5 @@
             <when value="false"/>
         </conditional>
     </xml>
-
 </macros>