Mercurial > repos > testtool > find_dmr
view findDMR/findDMR.xml @ 2:f13c6d0d664a draft
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author | testtool |
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date | Mon, 06 Feb 2017 09:58:23 -0500 |
parents | 3c3eb51a6414 |
children | 42cfcac7779d |
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<tool id="DMR" name="findDMR" version="1.16.2"> <requirements> <requirement type="package" version="3.2.1">R</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$IlmnTable" "$gmTable" "$cutoff" "$clusterSize" "$DMR"</command> <inputs> <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable"> <validator type="empty_field" message="This field is required."/> </param> <param optional="false" format="csv" name="IlmnTable" type="data" value="" help="CG, CHR, BP table." label="[required] IlmnTable"> <validator type="empty_field" message="This field is required."/> </param> <param optional="false" format="csv" name="gmTable" type="data" value="" help="gmSet of data." label="[required] gmTable"> <validator type="empty_field" message="This field is required."/> </param> <param name="cutoff" type="float" value="" label="Enter cutoff size (number)" help="e.g. '0.2'" > </param> <param name="clusterSize" type="float" value="" label="Enter cluster size (number)" help="e.g. '2'" > </param> </inputs> <outputs> <data format="bed" name="DMR" label="DMR.bed"/> </outputs> <tests> <test> <param name="test"> <element name="test-data"> <collection type="data"> <element name="GSMTable" value="test-data/input.csv"/> <element name="IlmnTable" value="test-data/IlmnTable.csv"/> <element name="gmTable" value="test-data/gmTable.csv"/> <element name="cutoff" value="0.2"/> <element name="clusterSize" value="2"/> </collection> </element> </param> <output format="bed" name="DMR" label="test-data/DMR.bed"/> </test> </tests> <help> **Description** </help> <citations> DMR </citations> </tool>