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