Mercurial > repos > jbrayet > ccat_1_0_docker

--- a/ccat_wrapper.py	Thu Jan 21 09:43:32 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,68 +0,0 @@
-#!/usr/bin/env python
-
-import sys, subprocess, tempfile, shutil, os.path
-
-def get_top_count( filename ):
-    for line in open( filename ):
-        if line.startswith( 'outputNum' ):
-            return int( line.split()[-1].strip() )
-
-def stop_err( tmp_dir, exception ):
-    print >> sys.stderr, "Error running CCAT."
-    shutil.rmtree( tmp_dir ) #some error has occurred, provide info and remove possibly non-empty temp directory
-    raise exception
-
-def main():
-    CCAT_BINARY = "/usr/bin/ccat/CCAT3.0/bin/CCAT"
-    input_tag_file = sys.argv[1]
-    input_control_file = sys.argv[2]
-    genome = sys.argv[3]
-    input_config_file = sys.argv[4]
-    project_name = sys.argv[5]
-    output_peak_file = sys.argv[6]
-    output_region_file = sys.argv[7]
-    output_top_file = sys.argv[8]
-    output_log_file = sys.argv[9]
-    root_dir = sys.argv[10]
-
-    ###### CREATE ANNOTATION FILES #########
-    databasePath = root_dir+"/database/files"
-
-    subprocess.Popen('mkdir -p '+databasePath+'/nebulaAnnotations', shell=True)
-    subprocess.Popen('mkdir -p '+databasePath+'/nebulaAnnotations/'+genome, shell=True)
-
-    nebulaGenomePath=databasePath+"/nebulaAnnotations/"+genome
-
-    FAIFILE='n'
-    LENFILE='n'
-    DICTFILE='n'
-    CHROFILE='n'
-    MAPFILE='n'
-
-    if not os.path.isfile(nebulaGenomePath+"/"+genome+".len"):
-        FAIFILE='y'
-        LENFILE='y'
-
-    FILEPATH=databasePath.replace("database/files","tool-data")
-
-    cmd='bash /usr/bin/create_annotation_files.sh '+FAIFILE+" "+LENFILE+" "+DICTFILE+" "+CHROFILE+" "+FILEPATH+" "+genome+" "+MAPFILE+" "+nebulaGenomePath
-    process=subprocess.Popen(cmd, shell=True)
-    process.wait()
-
-    chrom_info_file=nebulaGenomePath+"/"+genome+".len"
-
-    tmp_dir = tempfile.mkdtemp()
-    try:
-        proc = subprocess.Popen( args="%s %s > %s" % ( CCAT_BINARY, " ".join( map( lambda x: "%s" % x, [ input_tag_file, input_control_file, chrom_info_file, input_config_file, project_name ] ) ), output_log_file ), shell=True, cwd=tmp_dir )
-        proc.wait()
-        if proc.returncode:
-            raise Exception( "Error code: %i" % proc.returncode )
-        output_num = get_top_count( input_config_file )
-        shutil.move( os.path.join( tmp_dir, "%s.significant.peak" % project_name ), output_peak_file )
-        shutil.move( os.path.join( tmp_dir, "%s.significant.region" % project_name ), output_region_file )
-        shutil.move( os.path.join( tmp_dir, "%s.top%i.peak" % ( project_name, output_num ) ), output_top_file )
-    except Exception, e:
-        return stop_err( tmp_dir, e )
-    os.rmdir( tmp_dir ) #clean up empty temp working directory
-
-if __name__ == "__main__": main()
--- a/ccat_wrapper.xml	Thu Jan 21 09:43:32 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,130 +0,0 @@
-<tool id="peakcalling_ccat" name="CCAT" version="0.0.1">
-  <description>Control-based ChIP-seq Analysis Tool</description>
-  <requirements>
-  	<container type="docker">institutcuriengsintegration/ccat:1.0</container>
-  </requirements>
-  <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$genome'
-  #if str( $options_type[ 'options_type_selector' ] ) == 'advanced':
-  '$input_advanced_config_file'
-  #else:
-  '$options_type.input_config_file'
-  #end if
-  'CCAT'
-  '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file' '${__root_dir__}'</command>
-  <inputs>
-    <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" />
-    <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" />
-    <param name="genome" type="select" label="Genome" >
-        <option value="hg19" selected="True">Human (hg19)</option>
-        <option value="mm10" >Mouse (mm10)</option>
-        <option value="hg18" >Human (hg18)</option>
-        <option value="mm9" >Mouse (mm9)</option>
-    </param>
-    <conditional name="options_type">
-      <param name="options_type_selector" type="select" label="Advanced Options">
-        <option value="basic" selected="True">Hide Advanced Options and select configuration file</option>
-        <option value="advanced">Show Advanced Options</option>
-      </param>
-      <when value="basic">
-        <param name="input_config_file" type="data" format="txt" label="Select a pre-defined configuration file" />
-      </when>
-      <when value="advanced">
-        <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/>
-        <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/>
-        <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/>
-        <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" >
-          <option value="1">Transition from sense strand to anti-sense strand</option>
-          <option value="0" selected="True">Local maximum of read-enrichment profile</option>
-        </param>
-        <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/>
-        <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/>
-        <param name="random_seed" type="integer" label="Random Seed" value="123456"/>
-        <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/>
-        <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/>
-      </when>
-    </conditional>
-</inputs>
-  <outputs>
-    <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)">
-      <actions>
-        <action type="metadata" name="chromCol" default="1"/>
-        <action type="metadata" name="startCol" default="3"/>
-        <action type="metadata" name="endCol" default="4"/>
-      </actions>
-    </data>
-    <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)">
-      <actions>
-        <action type="metadata" name="chromCol" default="1"/>
-        <action type="metadata" name="startCol" default="3"/>
-        <action type="metadata" name="endCol" default="4"/>
-      </actions>
-    </data>
-    <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)">
-      <actions>
-        <action type="metadata" name="chromCol" default="1"/>
-        <action type="metadata" name="startCol" default="3"/>
-        <action type="metadata" name="endCol" default="4"/>
-      </actions>
-    </data>
-    <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
-  </outputs>
-  <configfiles>
-    <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced':
-fragmentSize	${options_type[ 'fragment_size' ]}
-slidingWinSize	${options_type[ 'sliding_window_size' ]}
-movingStep	${options_type[ 'moving_step' ]}
-isStrandSensitiveMode	${options_type[ 'is_strand_sensitive_mode' ]}
-minCount	${options_type[ 'min_count' ]}
-outputNum	${options_type[ 'output_num' ]}
-randomSeed	${options_type[ 'random_seed' ]}
-minScore	${options_type[ 'min_score' ]}
-bootstrapPass	${options_type[ 'bootstrap_pass' ]}
-#end if</configfile>
-  </configfiles>
-  <tests>
-    <test>
-      <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
-      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
-      <param name="options_type_selector" value="advanced" />
-      <param name="fragment_size" value="200" />
-      <param name="sliding_window_size" value="500" />
-      <param name="moving_step" value="50" />
-      <param name="is_strand_sensitive_mode" value="0" />
-      <param name="min_count" value="4" />
-      <param name="output_num" value="100000" />
-      <param name="random_seed" value="123456" />
-      <param name="min_score" value="5.0" />
-      <param name="bootstrap_pass" value="50" />
-      <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />
-      <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />
-      <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="True" />
-      <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
-    </test>
-    <test>
-      <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
-      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
-      <param name="options_type_selector" value="basic" />
-      <param name="input_config_file" value="ccat_3.0_histone_config" />
-      <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />
-      <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />
-      <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" />
-      <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
-    </test>
-  </tests>
-  <help>
-**What it does**
-
-This tool allows ChIP-seq peak/region calling using CCAT.
-
-View the original CCAT `documentation. &lt;http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.html&gt;`_
-
-------
-
-**Citation**
-
-For the underlying tool, please cite `Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20371496&gt;`_
-
-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
-
-  </help>
-</tool>
--- a/tool_dependencies.xml	Thu Jan 21 09:43:32 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="docker_ccat" version="0.1">
-        <repository changeset_revision="724ace069078" name="docker_ccat" owner="jbrayet" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>