Mercurial > repos > jetbrains > zinbra
changeset 6:7d532e820976
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 |
| files | tool_dependencies.xml zinbra.py zinbra.xml |
| diffstat | 3 files changed, 38 insertions(+), 16 deletions(-) [+] |
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--- a/tool_dependencies.xml Wed Oct 28 19:52:30 2015 +0300 +++ b/tool_dependencies.xml Wed Oct 28 20:08:20 2015 +0300 @@ -20,7 +20,6 @@ </install> <readme> Downloads epigenome integration JAR. - See for more details: https://teamcity.jetbrains.com/project.html?projectId=Epigenome_Tools&tab=projectOverview&guest=1 </readme> </package> </tool_dependency>
--- a/zinbra.py Wed Oct 28 19:52:30 2015 +0300 +++ b/zinbra.py Wed Oct 28 20:08:20 2015 +0300 @@ -1,7 +1,6 @@ #!/usr/bin/env python """ Python wrapper for zinbra.xml -Usage: zinbra.py "${genome}" "${bed}" "${bin}" "${fdr}" """ import os @@ -10,7 +9,14 @@ argv = sys.argv[1:] print 'Arguments {0}'.format(argv) -genome, bed, bin, fdr = argv + +# Check command +if len(argv) == 5: + genome, bin, fdr, action, bed = argv + assert action == "analyze" +else: + genome, bin, fdr, action, bed1, bed2 = argv + assert action == "compare" # Configure main jar path jar = os.environ.get("INTEGRATION_JAR") @@ -21,10 +27,11 @@ subprocess.check_call(cmd, cwd=None, shell=True) # See https://github.com/JetBrains-Research/zinbra for command line options -# cla.argument_string_list() is configured at ZinbraApplications#rebuildArgumentStringsFromVisualOptions -cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \ - 'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, - bed, - bin, fdr) +if action == "analyze": + cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \ + 'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed, bin, fdr) +else: + cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \ + 'compare -1 {1} -2 {2} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed1, bed2, bin, fdr) print 'Launching zinbra: {0}'.format(cmd) subprocess.check_call(cmd, cwd=None, shell=True)
--- a/zinbra.xml Wed Oct 28 19:52:30 2015 +0300 +++ b/zinbra.xml Wed Oct 28 20:08:20 2015 +0300 @@ -5,20 +5,36 @@ </requirements> <stdio> <!-- Wrapper ensures anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> + <exit_code range="1:"/> + <exit_code range=":-1"/> </stdio> <command interpreter="python"> - zinbra.py "${genome}" "${bed}" "${bin}" "${fdr}" + #if $action.selection == "analyze" + zinbra.py "${genome}" "${bin}" "${fdr}" analyze "${bed}" + #else + zinbra.py "${genome}" "${bin}" "${fdr}" compare "${bed1}" "${bed2}" + #end if </command> <inputs> - <param name="bed" type="data" format="bed" label="Aligned reads" description="BED Aligned reads to process" /> - <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference" /> - <param name="bin" size="5" type="integer" value="200" label="Bin size" /> - <param name="fdr" size="5" type="float" value="0.0001" label="FDR" /> + <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference"/> + <param name="bin" size="5" type="integer" value="200" label="Bin size"/> + <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/> + <conditional name="action"> + <param name="selection" type="select" label="Action"> + <option value="analyze">Compute enrichment of ChIP-Seq</option> + <option value="compare">Compare different ChIP-Seqs</option> + </param> + <when value="analyze"> + <param name="bed" type="data" format="bed" label="ChIP-Seq bed" description="BED Aligned reads to process"/> + </when> + <when value="compare"> + <param name="bed1" type="data" format="bed" label="ChIP-Seq bed1" description="BED Aligned reads 1 to process"/> + <param name="bed2" type="data" format="bed" label="ChIP-Seq bed2" description="BED Aligned reads 2 to process"/> + </when> + </conditional> </inputs> <outputs> - <data name="result" format="bed" label="result.bed" /> + <data name="result" format="bed" label="result.bed"/> </outputs> <help> Zinbra is a tool for analyzing and comparing ChIP-Seq data using Zero Inflated Negative Binomial Restricted Algorithm.