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author jetbrains
date Fri, 12 Oct 2018 06:02:38 -0400
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2:7140e1993b5b 3:13718f59d720
1 <tool id="cmeth" name="Cmeth" version="0.2.0">
2 <description>BS-Seq analysis</description>
3 <requirements>
4 <requirement type="package" version="0.0.1">integration_jar</requirement>
5 </requirements>
6 <stdio>
7 <!-- Wrapper ensures anything other than zero is an error -->
8 <exit_code range="1:"/>
9 <exit_code range=":-1"/>
10 </stdio>
11 <command interpreter="python">
12 #if $action.selection == "analyze"
13 cmeth_wrapper.py "${genome}" "${fdr}" analyze "${bam}"
14 #else
15 cmeth_wrapper.py "${genome}" "${fdr}" compare "${bam1}" "${bam2}"
16 #end if
17 </command>
18 <inputs>
19 <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference"/>
20 <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/>
21 <conditional name="action">
22 <param name="selection" type="select" label="Action">
23 <option value="analyze">Compute methylation</option>
24 <option value="compare">Compare methylation</option>
25 </param>
26 <when value="analyze">
27 <param name="bam" type="data" format="bam" label="Aligned BS-Seq bam" description="BAM BS-Seq Aligned reads to process"/>
28 </when>
29 <when value="compare">
30 <param name="bam1" type="data" format="bam" label="Aligned BS-Seq bam1" description="BAM BS-Seq Aligned reads to process 1"/>
31 <param name="bam2" type="data" format="bam" label="Aligned BS-Seq bam2" description="BAM BS-Seq Aligned reads to process 2"/>
32 </when>
33 </conditional>
34 </inputs>
35 <outputs>
36 #if $action.selection == "analyze"
37 <data name="result" format="csv" label="CG_unmethylated.csv"/>
38 #else
39 <data name="result" format="csv" label="CG_emr.csv"/>
40 #end if
41 </outputs>
42 <help>
43 Cmeth is a tool for analyzing and comparing cytosine methylation from WGBS (whole-genome bisulfite sequencing) data.
44 Both procedures rely on the nonparametric Bayesian switching HMM.
45 https://github.com/JetBrains-Research/cmeth
46 </help>
47 </tool>