Mercurial > repos > testtool > geo_data
comparison 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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32:be1ca0e7829b | 33:2c799524e1d3 |
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1 <tool id="DMR" name="findDMR" version="1.16.2"> | |
2 <description> | |
3 from series of samples | |
4 </description> | |
5 <requirements> | |
6 <requirement type="package" version="3.2.1">R</requirement> | |
7 </requirements> | |
8 <stdio> | |
9 <exit_code range="1:" /> | |
10 </stdio> | |
11 <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$platform" "$Data_Table" "$cutoff" "$clusterSize" "$DMR"</command> | |
12 <inputs> | |
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."/> | |
15 </param> | |
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."/> | |
18 </param> | |
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."/> | |
21 </param> | |
22 <param name="cutoff" type="float" value="" | |
23 label="Enter cutoff size (number)" | |
24 help="e.g. '0.2'" > | |
25 </param> | |
26 <param name="clusterSize" type="float" value="" | |
27 label="Enter cluster size (number)" | |
28 help="e.g. '2'" > | |
29 </param> | |
30 </inputs> | |
31 <outputs> | |
32 <data format="bed" name="DMR" label="DMR.bed"/> | |
33 </outputs> | |
34 <tests> | |
35 <test> | |
36 <param name="test"> | |
37 <element name="test-data"> | |
38 <collection type="data"> | |
39 <element name="GSMTable" value="test-data/input.txt"/> | |
40 <element name="platform" value="test-data/platform.txt"/> | |
41 <element name="Data_Table" value="test-data/Data_Table.txt"/> | |
42 <element name="cutoff" value="0.2"/> | |
43 <element name="clusterSize" value="2"/> | |
44 </collection> | |
45 </element> | |
46 </param> | |
47 <output format="bed" name="DMR" label="test-data/DMR.bed"/> | |
48 </test> | |
49 </tests> | |
50 <help> | |
51 **Description** | |
52 </help> | |
53 <citations> | |
54 DMR | |
55 </citations> | |
56 </tool> |