Mercurial > repos > jetbrains > zinbra
comparison zinbra.xml @ 10:eccf47de1192 draft default tip
Deleted selected files
| author | jetbrains |
|---|---|
| date | Fri, 12 Oct 2018 06:05:06 -0400 |
| parents | 0bf15064d38e |
| children |
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| 9:0bf15064d38e | 10:eccf47de1192 |
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| 1 <tool id="zinbra" name="Zinbra" version="0.0.1"> | |
| 2 <description>ChIP-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 $action.selection == "analyze" | |
| 13 zinbra_wrapper.py "${genome}" "${bin}" "${fdr}" analyze "${bed}" | |
| 14 #else | |
| 15 zinbra_wrapper.py "${genome}" "${bin}" "${fdr}" compare "${bed1}" "${bed2}" | |
| 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="bin" size="5" type="integer" value="200" label="Bin size"/> | |
| 21 <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> | |
| 35 </inputs> | |
| 36 <outputs> | |
| 37 <data name="result" format="bed" label="result.bed"/> | |
| 38 </outputs> | |
| 39 <help> | |
| 40 Zinbra is a tool for analyzing and comparing ChIP-Seq data using Zero Inflated Negative Binomial Restricted Algorithm. | |
| 41 https://github.com/JetBrains-Research/zinbra | |
| 42 </help> | |
| 43 </tool> |