isa2mzxml.xml

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<tool id="isa2mzxml" name="ISA to mzXML" version="1.3.0">

	<description>Extract mzXML files from an ISA dataset and output a collection of mzXML dataset.</description>

	<!-- Command {{{1 -->

	<command><![CDATA[
		## @@@BEGIN_CHEETAH@@@

		$__tool_directory__/extract-from-isa
		-i "$isa.extra_files_path"
		-e mzXML
		-o mzXML

		## @@@END_CHEETAH@@@
	]]></command>

	<!-- Inputs {{{1 -->

	<inputs>
		<param name="isa" label="ISA" type="data" format="isa-tab"/>
	</inputs>

	<!-- Outputs {{{1 -->

    <outputs>
		<collection name="mzXML" type="list" label="mzXML files">
			<discover_datasets pattern="(?P&lt;designation&gt;.+)\.[mM][zZ][xX][mM][lL]$" directory="mzXML" format="mzxml"/>
		</collection>
	</outputs>

	<!-- Tests {{{1 -->
	<tests>
		<test>
			<param name="isa" value="mzxml_study.zip" ftype="isa-tab"/>
			<output_collection name="mzXML" type="list" count="1">
				<element name="empty" file="mzxml_study_output/empty.mzXML" ftype="mzxml"/>
			</output_collection>
		</test>
	</tests>

	<!-- Help {{{1 -->
    <help>
<!-- @@@BEGIN_RST@@@ -->

====================
ISA to mzXML
====================

Extract mzXML files contained inside an ISA archive.

-----
Input
-----

ISA dataset
===========

The ISA-Tab dataset from which to extract the files.

------
Output
------

The output is a collection of mzXML files.

<!-- @@@END_RST@@@ -->
    </help>

	<!-- Citations {{{1 -->
    <citations>
        <citation type="doi">10.1038/ng.1054</citation> <!-- ISA -->
        <citation type="doi">10.1093/bioinformatics/btu813</citation> <!-- W4M -->
    </citations>

</tool>