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comparison zinbra.xml @ 6:7d532e820976

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Support comparison in zinbra. 3fba761
author oleg@oleg-desktop.times.labs.intellij.net
date Wed, 28 Oct 2015 20:08:20 +0300
parents ae6878068d07
children 617b5857ce96
comparison
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5:ae6878068d07 6:7d532e820976
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.0.1">epigenome</requirement> 4 <requirement type="package" version="0.0.1">epigenome</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <!-- Wrapper ensures anything other than zero is an error --> 7 <!-- Wrapper ensures anything other than zero is an error -->
8 <exit_code range="1:" /> 8 <exit_code range="1:"/>
9 <exit_code range=":-1" /> 9 <exit_code range=":-1"/>
10 </stdio> 10 </stdio>
11 <command interpreter="python"> 11 <command interpreter="python">
12 zinbra.py "${genome}" "${bed}" "${bin}" "${fdr}" 12 #if $action.selection == "analyze"
13 zinbra.py "${genome}" "${bin}" "${fdr}" analyze "${bed}"
14 #else
15 zinbra.py "${genome}" "${bin}" "${fdr}" compare "${bed1}" "${bed2}"
16 #end if
13 </command> 17 </command>
14 <inputs> 18 <inputs>
15 <param name="bed" type="data" format="bed" label="Aligned reads" description="BED Aligned reads to process" /> 19 <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference"/>
16 <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference" /> 20 <param name="bin" size="5" type="integer" value="200" label="Bin size"/>
17 <param name="bin" size="5" type="integer" value="200" label="Bin size" /> 21 <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/>
18 <param name="fdr" size="5" type="float" value="0.0001" label="FDR" /> 22 <conditional name="action">
23 <param name="selection" type="select" label="Action">
24 <option value="analyze">Compute enrichment of ChIP-Seq</option>
25 <option value="compare">Compare different ChIP-Seqs</option>
26 </param>
27 <when value="analyze">
28 <param name="bed" type="data" format="bed" label="ChIP-Seq bed" description="BED Aligned reads to process"/>
29 </when>
30 <when value="compare">
31 <param name="bed1" type="data" format="bed" label="ChIP-Seq bed1" description="BED Aligned reads 1 to process"/>
32 <param name="bed2" type="data" format="bed" label="ChIP-Seq bed2" description="BED Aligned reads 2 to process"/>
33 </when>
34 </conditional>
19 </inputs> 35 </inputs>
20 <outputs> 36 <outputs>
21 <data name="result" format="bed" label="result.bed" /> 37 <data name="result" format="bed" label="result.bed"/>
22 </outputs> 38 </outputs>
23 <help> 39 <help>
24 Zinbra is a tool for analyzing and comparing ChIP-Seq data using Zero Inflated Negative Binomial Restricted Algorithm. 40 Zinbra is a tool for analyzing and comparing ChIP-Seq data using Zero Inflated Negative Binomial Restricted Algorithm.
25 https://github.com/JetBrains-Research/zinbra 41 https://github.com/JetBrains-Research/zinbra
26 </help> 42 </help>