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annotate 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
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1 <tool id="zinbra" name="Zinbra" version="0.0.1">
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2 <description>ChIP-Seq enrichment</description>
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3 <requirements>
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4 <requirement type="package" version="0.0.1">epigenome</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 $action.selection == "analyze"
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13 zinbra.py "${genome}" "${bin}" "${fdr}" analyze "${bed}"
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14 #else
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15 zinbra.py "${genome}" "${bin}" "${fdr}" compare "${bed1}" "${bed2}"
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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="bin" size="5" type="integer" value="200" label="Bin size"/>
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21 <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/>
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22 <conditional name="action">
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23 <param name="selection" type="select" label="Action">
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24 <option value="analyze">Compute enrichment of ChIP-Seq</option>
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25 <option value="compare">Compare different ChIP-Seqs</option>
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26 </param>
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27 <when value="analyze">
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28 <param name="bed" type="data" format="bed" label="ChIP-Seq bed" description="BED Aligned reads to process"/>
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29 </when>
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30 <when value="compare">
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31 <param name="bed1" type="data" format="bed" label="ChIP-Seq bed1" description="BED Aligned reads 1 to process"/>
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32 <param name="bed2" type="data" format="bed" label="ChIP-Seq bed2" description="BED Aligned reads 2 to process"/>
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33 </when>
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34 </conditional>
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35 </inputs>
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36 <outputs>
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37 <data name="result" format="bed" label="result.bed"/>
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38 </outputs>
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39 <help>
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40 Zinbra is a tool for analyzing and comparing ChIP-Seq data using Zero Inflated Negative Binomial Restricted Algorithm.
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41 https://github.com/JetBrains-Research/zinbra
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42 </help>
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43 </tool>