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author testtool
date Sun, 11 Jun 2017 17:29:26 -0400
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1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="findDMP" name="findDMP" version="1.20.0">
3 <requirements>
4 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command> Rscript $__tool_directory__/findDMP.R "$input1" "$input2" "$output" </command>
10 <inputs>
11 <param format="RDdata" name="input1" type="data" label="Genomic Ratio Set" help="e.g. 'GRsetFromGEO tool output'"/>
12 <param format="csv" name="input2" type="data" label="Phenotype Table"
13 help="e.g.'ID Phenotype
14 GSM1255789 OLD
15 GSM1255798 OLD
16 GSM1255778 YOUNG'"/>
17 </inputs>
18 <outputs>
19 <data format="text" type="data" name="output" label="DMP.txt"/>
20 </outputs>
21 <tests>
22 <test>
23 <param name="test">
24 <element name="test-data">
25 <collection type="data">
26 <element name="input1" type="data" format="RData" label="test-data/out.RData"> </element>
27 <element name="input2" type="data" format="csv" label="test-data/OLDvsYOUNG.csv"> </element>
28 </collection>
29 </element>
30 </param>
31 <output name="output" type="data" format="text" label="test-data/DMP.txt"/>
32 </test>
33 </tests>
34 <help>
35 **What it does**
36 Tool finds differentially methylated positions (DMPs) with respect to a phenotype covariate
37 **Input**
38 GenomicRatioSet object
39 Phenotype Table
40 **Output**
41 Text file containing differentially methylated positions
42 </help>
43 <citations>
44 <citation type="doi">10.1093/bioinformatics/btu049</citation>
45 </citations>
46 </tool>