# HG changeset patch
# User jetbrains
# Date 1539338558 14400
# Node ID 13718f59d7207127d7e2bc828242bc35314e8510
# Parent  7140e1993b5bee34f76ce5c3cd66b125ba380604
Deleted selected files

diff -r 7140e1993b5b -r 13718f59d720 cmeth.xml
--- 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>
diff -r 7140e1993b5b -r 13718f59d720 cmeth_wrapper.py
--- 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)
diff -r 7140e1993b5b -r 13718f59d720 tool_dependencies.xml
--- 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>