Mercurial > repos > jetbrains > cmeth
changeset 3:13718f59d720 draft default tip
Deleted selected files
| author | jetbrains |
|---|---|
| date | Fri, 12 Oct 2018 06:02:38 -0400 |
| parents | 7140e1993b5b |
| children | |
| files | cmeth.xml cmeth_wrapper.py tool_dependencies.xml |
| diffstat | 3 files changed, 0 insertions(+), 107 deletions(-) [+] |
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--- a/cmeth.xml Thu Nov 12 12:01:00 2015 +0300 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,47 +0,0 @@ -<tool id="cmeth" name="Cmeth" version="0.2.0"> - <description>BS-Seq analysis</description> - <requirements> - <requirement type="package" version="0.0.1">integration_jar</requirement> - </requirements> - <stdio> - <!-- Wrapper ensures anything other than zero is an error --> - <exit_code range="1:"/> - <exit_code range=":-1"/> - </stdio> - <command interpreter="python"> - #if $action.selection == "analyze" - cmeth_wrapper.py "${genome}" "${fdr}" analyze "${bam}" - #else - cmeth_wrapper.py "${genome}" "${fdr}" compare "${bam1}" "${bam2}" - #end if - </command> - <inputs> - <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference"/> - <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 methylation</option> - <option value="compare">Compare methylation</option> - </param> - <when value="analyze"> - <param name="bam" type="data" format="bam" label="Aligned BS-Seq bam" description="BAM BS-Seq Aligned reads to process"/> - </when> - <when value="compare"> - <param name="bam1" type="data" format="bam" label="Aligned BS-Seq bam1" description="BAM BS-Seq Aligned reads to process 1"/> - <param name="bam2" type="data" format="bam" label="Aligned BS-Seq bam2" description="BAM BS-Seq Aligned reads to process 2"/> - </when> - </conditional> - </inputs> - <outputs> - #if $action.selection == "analyze" - <data name="result" format="csv" label="CG_unmethylated.csv"/> - #else - <data name="result" format="csv" label="CG_emr.csv"/> - #end if - </outputs> - <help> -Cmeth is a tool for analyzing and comparing cytosine methylation from WGBS (whole-genome bisulfite sequencing) data. -Both procedures rely on the nonparametric Bayesian switching HMM. -https://github.com/JetBrains-Research/cmeth - </help> -</tool>
--- a/cmeth_wrapper.py Thu Nov 12 12:01:00 2015 +0300 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -#!/usr/bin/env python - -import os -import sys -import subprocess - -argv = sys.argv[1:] -print 'Arguments {0}'.format(argv) - -# Check command -if len(argv) == 4: - genome, fdr, action, bam = argv - assert action == "analyze" -else: - genome, fdr, action, bam1, bam2 = argv - assert action == "compare" - -# Configure main jar path -jar = os.environ.get("INTEGRATION_JAR") -print 'Using JAR distributive file {0}'.format(jar) - -cmd = 'java -cp {0} org.jetbrains.bio.genestack.FastaToTwoBitCLA {1} reference.2bit'.format(jar, genome) -print 'Converting reference genome fasta to 2bit: {0}'.format(cmd) -subprocess.check_call(cmd, cwd=None, shell=True) - -# See https://github.com/JetBrains-Research/cmeth for command line options -if action == "analyze": - cmd = 'java -cp {0} org.jetbrains.bio.cmeth.CmethCLA ' \ - 'analyze -i {1} -r reference.2bit -fdr {2}'.format(jar, bam, fdr) -else: - cmd = 'java -cp {0} org.jetbrains.bio.cmeth.CmethCLA ' \ - 'compare -1 {1} -2 {2} -r reference.2bit -fdr {3}'.format(jar, bam1, bam2, fdr) -print 'Launching cmeth: {0}'.format(cmd) -subprocess.check_call(cmd, cwd=None, shell=True)
--- a/tool_dependencies.xml Thu Nov 12 12:01:00 2015 +0300 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <!-- - Package for downloading latest successful development tools. - Tags information is here: - https://wiki.galaxyproject.org/ToolDependenciesTagSets - --> - <package name="integration_jar" version="0.0.1" prior_installation_required="True"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://teamcity.jetbrains.com/guestAuth/repository/download/Epigenome_Tools_Integration/lastSuccessful/integration-dev-all.jar</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/</destination_directory> - </action> - <!-- Set environment variable $INTEGRATION_JAR so Python script knows where to look --> - <action type="set_environment"> - <environment_variable name="$INTEGRATION_JAR" action="set_to">$INSTALL_DIR/integration-dev-all.jar</environment_variable> - </action> - </actions> - </install> - <readme> - Downloads epigenome integration JAR. - </readme> - </package> -</tool_dependency>