Mercurial > repos > prog > isaextractor
diff isa2mzdata.xml @ 0:975585306dc4 draft default tip
"planemo upload commit c2694fb4aa55c4f25eb53db73496eaf5e56d7872"
author | prog |
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date | Wed, 08 Jan 2020 07:50:13 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/isa2mzdata.xml Wed Jan 08 07:50:13 2020 -0500 @@ -0,0 +1,77 @@ +<!-- vi: se fdm=marker : --> +<tool id="isa2mzdata" name="ISA to mzData" version="1.3.0"> + + <description>Extract mzData files from an ISA dataset and output a collection of mzData dataset.</description> + + <!-- Command {{{1 --> + + <command><![CDATA[ + ## @@@BEGIN_CHEETAH@@@ + + $__tool_directory__/extract-from-isa + -i "$isa.extra_files_path" + -e mzData + -o mzData + + ## @@@END_CHEETAH@@@ + ]]></command> + + <!-- Inputs {{{1 --> + + <inputs> + <param name="isa" label="ISA" type="data" format="isa-tab"/> + </inputs> + + <!-- Outputs {{{1 --> + + <outputs> + <collection name="mzData" type="list" label="mzData files"> + <discover_datasets pattern="(?P<designation>.+)\.[mM][zZ][dD][aA][tT][aA]$" directory="mzData" format="mzdata"/> + </collection> + </outputs> + + <!-- Tests {{{1 --> + <tests> + <test> + <param name="isa" value="mzdata_study.zip" ftype="isa-tab"/> + <output_collection name="mzData" type="list" count="1"> + <element name="empty" file="mzdata_study_output/empty.mzData" ftype="mzdata"/> + </output_collection> + </test> + </tests> + + <!-- Help {{{1 --> + <help> +<!-- @@@BEGIN_RST@@@ --> + +==================== +ISA to mzData +==================== + +Extract mzData 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 mzData 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>