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1 <tool id="findDMR" name="findDMR" version="1.16.2">
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2 <requirements>
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3 <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
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4 </requirements>
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5 <stdio>
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6 <exit_code range="1:" />
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7 </stdio>
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8 <command> Rscript $__tool_directory__/findDMR.R "$input1" "$input2" "$output" </command>
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9 <inputs>
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10 <param name="input1" type="data" format="Rdata" label="GenomicRatioSet.Rdata" help="e.g. 'GSE51547'"/>
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11 <param name="input2" type="data" format="txt" label="PhenoTab.txt" help="ID and Phenotype table"/>
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12 </inputs>
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13 <outputs>
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14 <data format="txt" name="output" label="findDMR.txt"/>
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="test">
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19 <element name="test-data"/>
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20 <collection type="data">
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21 <element format="Rdata" name="input1" label="test-data/GenomicRatioSet.Rdata"/>
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22 <element format="txt" name="input2" label="test-data/PhenoTab.txt"/>
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23 </collection>
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24 </param>
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25 <output format="txt" name="output" label="test-data/findDMR.txt"/>
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26 </test>
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27 </tests>
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28 <help>
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29 Identify CpGs where methylation is associated with a continuous or categorical phenotype.
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30 </help>
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31 <citations>
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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.
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33 </citations>
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34 </tool>
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