# HG changeset patch
# User jbrayet
# Date 1453392277 18000
# Node ID cef20aef8bbe1274f19986683dbbd2cc8c34a003
# Parent a11ad774a6b142e95f92cbfb27af618bd6631638
Deleted selected files
diff -r a11ad774a6b1 -r cef20aef8bbe ccat_wrapper.py
--- a/ccat_wrapper.py Thu Jan 21 10:53:13 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()
diff -r a11ad774a6b1 -r cef20aef8bbe ccat_wrapper.xml
--- a/ccat_wrapper.xml Thu Jan 21 10:53:13 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,130 +0,0 @@
-
- Control-based ChIP-seq Analysis Tool
-
- institutcuriengsintegration/ccat:1.0
-
- 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__}'
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- #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
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-**What it does**
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-This tool allows ChIP-seq peak/region calling using CCAT.
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-View the original CCAT `documentation. <http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.html>`_
-
-------
-
-**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. <http://www.ncbi.nlm.nih.gov/pubmed/20371496>`_
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-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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diff -r a11ad774a6b1 -r cef20aef8bbe tool_dependencies.xml
--- a/tool_dependencies.xml Thu Jan 21 10:53:13 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
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