Mercurial > repos > testtool > geo_data
diff findDMR/findDMR.xml @ 33:2c799524e1d3 draft
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author | testtool |
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date | Fri, 14 Apr 2017 06:44:35 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findDMR/findDMR.xml Fri Apr 14 06:44:35 2017 -0400 @@ -0,0 +1,56 @@ +<tool id="DMR" name="findDMR" version="1.16.2"> + <description> +from series of samples + </description> + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + </requirements> +<stdio> + <exit_code range="1:" /> +</stdio> + <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$platform" "$Data_Table" "$cutoff" "$clusterSize" "$DMR"</command> + <inputs> + <param optional="false" format="txt" 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="txt" name="platform" type="data" value="" help="CG, CHR, BP table." label="[required] platform"> + <validator type="empty_field" message="This field is required."/> + </param> + <param optional="false" format="txt" name="Data_Table" type="data" value="" help="Matrix of data." label="[required] Data_Table"> + <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.txt"/> + <element name="platform" value="test-data/platform.txt"/> + <element name="Data_Table" value="test-data/Data_Table.txt"/> + <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>