view isa2mzml.xml @ 0:975585306dc4 draft default tip

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<!-- vi: se fdm=marker : -->
<tool id="isa2mzml" name="ISA to mzML" version="1.3.0">

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

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

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

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

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

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

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

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

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

	<!-- Tests {{{1 -->
	<tests>
		<test>
			<param name="isa" value="mzml_study.zip" ftype="isa-tab"/>
			<output_collection name="mzML" type="list" count="1">
				<element name="empty" file="mzml_study_output/empty.mzML" ftype="mzml"/>
			</output_collection>
		</test>
	</tests>

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

====================
ISA to mzML
====================

Extract mzML 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 mzML 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>