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comparison findDMR/findDMR.xml @ 12:083895dbc289 draft

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author testtool
date Mon, 12 Jun 2017 11:05:04 -0400
parents 7df2b7d79391
children 3735f4bd0a2d
comparison
equal deleted inserted replaced
11:24ac6f93cc3e 12:083895dbc289
1 <tool id="DMR" name="findDMR" version="1.16.2"> 1 <tool id="findDMR" name="findDMR" version="1.16.2">
2 <description>
3 from series of samples
4 </description>
5 <requirements> 2 <requirements>
6 <requirement type= "package" version="0.0.1">450kdependency</requirement> 3 <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
7 <requirement type="package" version="3.2.1">R</requirement> 4 </requirements>
8 </requirements>
9 <stdio> 5 <stdio>
10 <exit_code range="1:" /> 6 <exit_code range="1:" />
11 </stdio> 7 </stdio>
12 <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$platform" "$Data_Table" "$cutoff" "$clusterSize" "$DMR"</command> 8 <command> Rscript $__tool_directory__/findDMR.R "$input1" "$input2" "$output" </command>
13 <inputs> 9 <inputs>
14 <param optional="false" format="txt" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable"> 10 <param name="input1" format="Rdata" label="GenomicRatioSet.Rdata" help="e.g. 'GSE51547'"/>
15 <validator type="empty_field" message="This field is required."/> 11 <param name="input2" format="txt" label="PhenoTab.txt" help="ID and Phenotype table"/>
16 </param>
17 <param optional="false" format="txt" name="platform" type="data" value="" help="CG, CHR, BP table." label="[required] platform">
18 <validator type="empty_field" message="This field is required."/>
19 </param>
20 <param optional="false" format="txt" name="Data_Table" type="data" value="" help="Matrix of data." label="[required] Data_Table">
21 <validator type="empty_field" message="This field is required."/>
22 </param>
23 <param name="cutoff" type="float" value=""
24 label="Enter cutoff size (number)"
25 help="e.g. '0.2'" >
26 </param>
27 <param name="clusterSize" type="float" value=""
28 label="Enter cluster size (number)"
29 help="e.g. '2'" >
30 </param>
31 </inputs> 12 </inputs>
32 <outputs> 13 <outputs>
33 <data format="bed" name="DMR" label="DMR.bed"/> 14 <data format="txt" name="output" label="findDMR.txt"/>
34 </outputs> 15 </outputs>
35 <tests> 16 <tests>
36 <test> 17 <test>
37 <param name="test"> 18 <param name="test">
38 <element name="test-data"> 19 <element name="test-data"/>
39 <collection type="data"> 20 <collection type="data">
40 <element name="GSMTable" value="test-data/input.txt"/> 21 <element format="Rdata" name="input1" label="test-data/GenomicRatioSet.Rdata"/>
41 <element name="platform" value="test-data/platform.txt"/> 22 <element format="txt" name="input2" label="test-data/PhenoTab.txt"/>
42 <element name="Data_Table" value="test-data/Data_Table.txt"/>
43 <element name="cutoff" value="0.2"/>
44 <element name="clusterSize" value="2"/>
45 </collection> 23 </collection>
46 </element>
47 </param> 24 </param>
48 <output format="bed" name="DMR" label="test-data/DMR.bed"/> 25 <output format="txt" name="output" label="test-data/findDMR.txt"/>
49 </test> 26 </test>
50 </tests> 27 </tests>
51 <help> 28 <help>
52 **Description** 29 Identify CpGs where methylation is associated with a continuous or categorical phenotype.
53 </help> 30 </help>
54 <citations> 31 <citations>
55 DMR 32 Aryee, Martin J., et al. "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays." Bioinformatics 30.10 (2014): 1363-1369.
56 </citations> 33 </citations>
57 </tool> 34 </tool>