Mercurial > repos > jetbrains > cmeth
comparison cmeth.xml @ 0:d7714f886224
Initial commit. Snapshot 61f45be
author | oleg@oleg-desktop |
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date | Thu, 29 Oct 2015 12:04:47 +0300 |
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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> |