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1 <tool id="cmeth" name="Cmeth" version="0.2.0">
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2 <description>BS-Seq analysis</description>
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3 <requirements>
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4 <requirement type="package" version="0.0.1">integration_jar</requirement>
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5 </requirements>
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6 <stdio>
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7 <!-- Wrapper ensures anything other than zero is an error -->
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8 <exit_code range="1:"/>
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9 <exit_code range=":-1"/>
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10 </stdio>
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11 <command interpreter="python">
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12 #if $action.selection == "analyze"
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13 cmeth_wrapper.py "${genome}" "${fdr}" analyze "${bam}"
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14 #else
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15 cmeth_wrapper.py "${genome}" "${fdr}" compare "${bam1}" "${bam2}"
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16 #end if
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17 </command>
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18 <inputs>
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19 <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference"/>
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20 <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/>
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21 <conditional name="action">
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22 <param name="selection" type="select" label="Action">
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23 <option value="analyze">Compute methylation</option>
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24 <option value="compare">Compare methylation</option>
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25 </param>
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26 <when value="analyze">
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27 <param name="bam" type="data" format="bam" label="Aligned BS-Seq bam" description="BAM BS-Seq Aligned reads to process"/>
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28 </when>
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29 <when value="compare">
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30 <param name="bam1" type="data" format="bam" label="Aligned BS-Seq bam1" description="BAM BS-Seq Aligned reads to process 1"/>
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31 <param name="bam2" type="data" format="bam" label="Aligned BS-Seq bam2" description="BAM BS-Seq Aligned reads to process 2"/>
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32 </when>
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33 </conditional>
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34 </inputs>
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35 <outputs>
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36 #if $action.selection == "analyze"
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37 <data name="result" format="csv" label="CG_unmethylated.csv"/>
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38 #else
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39 <data name="result" format="csv" label="CG_emr.csv"/>
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40 #end if
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41 </outputs>
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42 <help>
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43 Cmeth is a tool for analyzing and comparing cytosine methylation from WGBS (whole-genome bisulfite sequencing) data.
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44 Both procedures rely on the nonparametric Bayesian switching HMM.
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45 https://github.com/JetBrains-Research/cmeth
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46 </help>
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47 </tool>
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