Mercurial > repos > testtool > find_dmr

comparison findDMR/findDMR.xml @ 5:715d03e1fd83 draft

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author testtool
date Mon, 20 Mar 2017 06:51:59 -0400
parents 0d1957068766
children a0e3f4efb03f
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4:0d1957068766 5:715d03e1fd83
8 <stdio> 8 <stdio>
9 <exit_code range="1:" /> 9 <exit_code range="1:" />
10 </stdio> 10 </stdio>
11 <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$platform" "$Data_Table" "$cutoff" "$clusterSize" "$DMR"</command> 11 <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$platform" "$Data_Table" "$cutoff" "$clusterSize" "$DMR"</command>
12 <inputs> 12 <inputs>
13 <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable"> 13 <param optional="false" format="txt" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable">
14 <validator type="empty_field" message="This field is required."/> 14 <validator type="empty_field" message="This field is required."/>
15 </param> 15 </param>
16 <param optional="false" format="csv" name="platform" type="data" value="" help="CG, CHR, BP table." label="[required] platform"> 16 <param optional="false" format="txt" name="platform" type="data" value="" help="CG, CHR, BP table." label="[required] platform">
17 <validator type="empty_field" message="This field is required."/> 17 <validator type="empty_field" message="This field is required."/>
18 </param> 18 </param>
19 <param optional="false" format="csv" name="Data_Table" type="data" value="" help="Matrix of data." label="[required] Data_Table"> 19 <param optional="false" format="txt" name="Data_Table" type="data" value="" help="Matrix of data." label="[required] Data_Table">
20 <validator type="empty_field" message="This field is required."/> 20 <validator type="empty_field" message="This field is required."/>
21 </param> 21 </param>
22 <param name="cutoff" type="float" value="" 22 <param name="cutoff" type="float" value=""
23 label="Enter cutoff size (number)" 23 label="Enter cutoff size (number)"
24 help="e.g. '0.2'" > 24 help="e.g. '0.2'" >
34 <tests> 34 <tests>
35 <test> 35 <test>
36 <param name="test"> 36 <param name="test">
37 <element name="test-data"> 37 <element name="test-data">
38 <collection type="data"> 38 <collection type="data">
39 <element name="GSMTable" value="test-data/input.csv"/> 39 <element name="GSMTable" value="test-data/input.txt"/>
40 <element name="platform" value="test-data/platform.csv"/> 40 <element name="platform" value="test-data/platform.txt"/>
41 <element name="Data_Table" value="test-data/Data_Table.csv"/> 41 <element name="Data_Table" value="test-data/Data_Table.txt"/>
42 <element name="cutoff" value="0.2"/> 42 <element name="cutoff" value="0.2"/>
43 <element name="clusterSize" value="2"/> 43 <element name="clusterSize" value="2"/>
44 </collection> 44 </collection>
45 </element> 45 </element>
46 </param> 46 </param>