Mercurial > repos > pjbriggs > macs21
changeset 1:d0986d2be693 draft
Substantial reimplementation of internals, also renamed id and version.
| author | pjbriggs |
|---|---|
| date | Thu, 29 Jan 2015 11:11:21 -0500 |
| parents | fdad0c8c0957 |
| children | 15889783e759 |
| files | macs21_wrapper.py macs21_wrapper.xml tool_dependencies.xml |
| diffstat | 3 files changed, 259 insertions(+), 318 deletions(-) [+] |
line wrap: on
line diff
--- a/macs21_wrapper.py Wed Jan 21 11:07:37 2015 -0500 +++ b/macs21_wrapper.py Thu Jan 29 11:11:21 2015 -0500 @@ -1,208 +1,177 @@ -#purpose: macs2 python wrapper -#author: Ziru Zhou -#date: November, 2012 +#!/bin/env python +# +# Galaxy wrapper to run MACS 2.1 +# +# Completely rewritten from the original macs2 wrapped by Ziru Zhou +# taken from http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 -import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip -from galaxy import eggs -import pkg_resources -pkg_resources.require( "simplejson" ) -import simplejson +import sys +import os +import subprocess +import tempfile +import shutil -CHUNK_SIZE = 1024 +def move_file(working_dir,name,destination): + """Move a file 'name' from 'working_dir' to 'destination' + + """ + if destination is None: + # Nothing to do + return + source = os.path.join(working_dir,name) + if os.path.exists(source): + shutil.move(source,destination) -#========================================================================================== -#functions -#========================================================================================== -def gunzip_cat_glob_path( glob_path, target_filename, delete = False ): - out = open( target_filename, 'wb' ) - for filename in glob.glob( glob_path ): - fh = gzip.open( filename, 'rb' ) - while True: - data = fh.read( CHUNK_SIZE ) - if data: - out.write( data ) - else: - break - fh.close() - if delete: - os.unlink( filename ) - out.close() +def convert_xls_to_interval(xls_file,interval_file,header=None): + """Convert MACS XLS file to interval + + From the MACS readme: "Coordinates in XLS is 1-based which is different with + BED format." -def xls_to_interval( xls_file, interval_file, header = None ): - out = open( interval_file, 'wb' ) + However this function no longer performs any coordinate conversions, it + simply ensures that any blank or non-data lines are commented out + + """ + fp = open(interval_file,'wb') if header: - out.write( '#%s\n' % header ) - wrote_header = False - #From macs readme: Coordinates in XLS is 1-based which is different with BED format. - #PJB: updated to keep original 'start' coordinate i.e. do not convert to BED - for line in open( xls_file ): - #keep all existing comment lines - if line.startswith( '#' ): - out.write( line ) - #added for macs2 since there is an extra newline - ##elif line.startswith( '\n' ): - ## out.write( line ) - elif not wrote_header: - out.write( '#%s' % line ) - print line - wrote_header = True + fp.write('#%s\n' % header) + for line in open(xls_file): + # Keep all existing comment lines + if line.startswith('#'): + fp.write(line) else: - fields = line.split( '\t' ) - if len( fields ) > 1: + # Split line into fields and test to see if + # the 'start' field is actually an integer + fields = line.split('\t') + if len(fields) > 1: try: - # Try to convert 'start' to int and shift - ##fields[1] = str( int( fields[1] ) - 1 ) - # PJB don't correct, just test to see if it's an integer - int( fields[1] ) + int(fields[1]) except ValueError: # Integer conversion failed so comment out # "bad" line instead fields[0] = "#%s" % fields[0] - out.write( '\t'.join( fields ) ) - out.close() - -#========================================================================================== -#main -#========================================================================================== -def main(): - #take in options file and output file names - options = simplejson.load( open( sys.argv[1] ) ) - outputs = simplejson.load( open( sys.argv[2] ) ) + fp.write( '\t'.join( fields ) ) + fp.close() - #================================================================================= - #parse options and execute macs2 - #================================================================================= - #default inputs that are in every major command - experiment_name = '_'.join( options['experiment_name'].split() ) #save experiment name here, it will be used by macs for some file names - cmdline = "macs2 %s -t %s" % ( options['command'], ",".join( options['input_chipseq'] ) ) - if options['input_control']: - cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) ) +if __name__ == "__main__": - #================================================================================= - if (options['command'] == "callpeak"): - output_summits_bed = outputs['output_summits_bed_file'] - output_extra_html = outputs['output_extra_file'] - output_extra_path = outputs['output_extra_file_path'] - output_peaks = outputs['output_peaks_file'] - output_narrowpeaks = outputs['output_narrowpeaks_file'] - output_broadpeaks = outputs['output_broadpeaks_file'] - output_gappedpeaks = outputs['output_gappedpeaks_file'] - output_xls_to_interval_peaks_file = outputs['output_xls_to_interval_peaks_file'] - output_treat_pileup = outputs['output_treat_pileup_file'] - output_lambda_bedgraph = outputs['output_lambda_bedgraph_file'] + # Echo the command line + print ' '.join(sys.argv) - cmdline = "%s --format='%s' --name='%s' --gsize='%s' --bw='%s'" % ( cmdline, options['format'], experiment_name, options['gsize'], options['bw'] ) - if (options['broad'] == 'broad'): - cmdline = "%s --broad --broad-cutoff='%s'" % ( cmdline, options['broad_cutoff'] ) - if 'pvalue' in options: - cmdline = "%s --pvalue='%s'" % ( cmdline, options['pvalue'] ) - elif 'qvalue' in options: - cmdline = "%s --qvalue='%s'" % ( cmdline, options['qvalue'] ) - cmdline = "%s --mfold %s %s %s %s %s %s --keep-dup %s" % (cmdline, options['mfoldlo'], options['mfoldhi'], options['nolambda'], options['bdg'], options['spmr'], options['call_summits'], options['keep_dup'] ) - - if 'nomodel' in options: - cmdline = "%s --nomodel --extsize='%s'" % ( cmdline, options['nomodel'] ) - #================================================================================= - if (options['command'] == "bdgcmp"): - output_bdgcmp = outputs['output_bdgcmp_file'] - - cmdline = "%s -m %s -p %s -o bdgcmp_out.bdg" % ( cmdline, options['m'], options['pseudocount'] ) - #================================================================================= + # Initialise output files - values are set by reading from + # the command line supplied by the Galaxy wrapper + output_extra_html = None + output_extra_path = None + output_broadpeaks = None + output_gappedpeaks = None + output_narrowpeaks = None + output_treat_pileup = None + output_lambda_bedgraph = None + output_xls_to_interval_peaks_file = None + output_peaks = None + output_bdgcmp = None - tmp_dir = tempfile.mkdtemp() #macs makes very messy output, need to contain it into a temp dir, then provide to user - stderr_name = tempfile.NamedTemporaryFile().name # redirect stderr here, macs provides lots of info via stderr, make it into a report - proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) ) - proc.wait() - #We don't want to set tool run to error state if only warnings or info, e.g. mfold could be decreased to improve model, but let user view macs log - #Do not terminate if error code, allow dataset (e.g. log) creation and cleanup - if proc.returncode: - stderr_f = open( stderr_name ) - while True: - chunk = stderr_f.read( CHUNK_SIZE ) - if not chunk: - stderr_f.close() - break - sys.stderr.write( chunk ) - - #================================================================================= - #copy files created by macs2 to appripriate directory with the provided names - #================================================================================= + # Build the MACS 2.1 command line + # Initial arguments are always the same: command & input ChIP-seq file name + cmdline = ["macs2 %s -t %s" % (sys.argv[1],sys.argv[2])] - #================================================================================= - #move files generated by callpeak command - if (options['command'] == "callpeak"): - #run R to create pdf from model script - if os.path.exists( os.path.join( tmp_dir, "%s_model.r" % experiment_name ) ): - cmdline = 'R --vanilla --slave < "%s_model.r" > "%s_model.r.log"' % ( experiment_name, experiment_name ) - proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir ) - proc.wait() - - #move bed out to proper output file - created_bed_name = os.path.join( tmp_dir, "%s_summits.bed" % experiment_name ) - if os.path.exists( created_bed_name ): - shutil.move( created_bed_name, output_summits_bed ) - - #OICR peak_xls file - created_peak_xls_file = os.path.join( tmp_dir, "%s_peaks.xls" % experiment_name ) - if os.path.exists( created_peak_xls_file ): - # shutil.copy( created_peak_xls_file, os.path.join ( "/mnt/galaxyData/tmp/", "%s_peaks.xls" % ( os.path.basename(output_extra_path) ))) - shutil.copyfile( created_peak_xls_file, output_peaks ) - - #peaks.encodepeaks (narrowpeaks) file - created_narrowpeak_file = os.path.join (tmp_dir, "%s_peaks.narrowPeak" % experiment_name ) - if os.path.exists( created_narrowpeak_file ): - shutil.move (created_narrowpeak_file, output_narrowpeaks ) - - #peaks.broadpeaks file - created_broadpeak_file = os.path.join (tmp_dir, "%s_peaks.broadPeak" % experiment_name ) - if os.path.exists( created_broadpeak_file ): - shutil.move (created_broadpeak_file, output_broadpeaks ) - - #peaks.gappedpeaks file - created_gappedpeak_file = os.path.join (tmp_dir, "%s_peaks.gappedPeak" % experiment_name ) - if os.path.exists( created_gappedpeak_file ): - shutil.move (created_gappedpeak_file, output_gappedpeaks ) + # Process remaining args + for arg in sys.argv[3:]: + if arg.startswith('--format='): + # Convert format to uppercase + format_ = arg.split('=')[1].upper() + cmdline.append("--format=%s" % format_) + elif arg.startswith('--name='): + # Replace whitespace in name with underscores + experiment_name = '_'.join(arg.split('=')[1].split()) + cmdline.append("--name=%s" % experiment_name) + elif arg.startswith('--output-'): + # Handle destinations for output files + arg0,filen = arg.split('=') + if arg0 == '--output-summits': + output_summits = filen + elif arg0 == '--output-extra-files': + output_extra_html = filen + elif arg0 == '--output-extra-files-path': + output_extra_path = filen + elif arg0 == '--output-broadpeaks': + output_broadpeaks = filen + elif arg0 == '--output-gappedpeaks': + output_gappedpeaks = filen + elif arg0 == '--output-narrowpeaks': + output_narrowpeaks = filen + elif arg0 == '--output-pileup': + output_treat_pileup = filen + elif arg0 == '--output-lambda-bedgraph': + output_lambda_bedgraph = filen + elif arg0 == '--output-xls-to-interval': + output_xls_to_interval_peaks_file = filen + elif arg0 == '--output-peaks': + output_peaks = filen + else: + # Pass remaining args directly to MACS + # command line + cmdline.append(arg) + + cmdline = ' '.join(cmdline) + print "Generated command line:\n%s" % cmdline - #parse xls files to interval files as needed - #if 'xls_to_interval' in options: - if (options['xls_to_interval'] == "True"): - create_peak_xls_file = os.path.join( tmp_dir, '%s_peaks.xls' % experiment_name ) - if os.path.exists( create_peak_xls_file ): - xls_to_interval( create_peak_xls_file, output_xls_to_interval_peaks_file, header = 'peaks file' ) - - #bedgraph bedgraph files - if (options['bdg']): - created_treat_pileup_file = os.path.join (tmp_dir, "%s_treat_pileup.bdg" % experiment_name ) - if os.path.exists( created_treat_pileup_file ): - shutil.move (created_treat_pileup_file, output_treat_pileup ) - created_lambda_bedgraph_file = os.path.join (tmp_dir, "%s_control_lambda.bdg" % experiment_name ) - if os.path.exists( created_lambda_bedgraph_file ): - shutil.move (created_lambda_bedgraph_file, output_lambda_bedgraph ) + # Execute MACS2 + # + # Make a working directory + working_dir = tempfile.mkdtemp() + # + # Collect stderr in a file for reporting later + stderr_filen = tempfile.NamedTemporaryFile().name + # + # Run MACS2 + proc = subprocess.Popen(args=cmdline,shell=True,cwd=working_dir, + stderr=open(stderr_filen,'wb')) + proc.wait() + + # Run R script to create PDF from model script + if os.path.exists(os.path.join(working_dir,"%s_model.r" % experiment_name)): + cmdline = 'R --vanilla --slave < "%s_model.r" > "%s_model.r.log"' % \ + (experiment_name, experiment_name) + proc = subprocess.Popen(args=cmdline,shell=True,cwd=working_dir) + proc.wait() - #move all remaining files to extra files path of html file output to allow user download - out_html = open( output_extra_html, 'wb' ) - out_html.write( '<html><head><title>Additional output created by MACS (%s)</title></head><body><h3>Additional Files:</h3><p><ul>\n' % experiment_name ) - os.mkdir( output_extra_path ) - for filename in sorted( os.listdir( tmp_dir ) ): - shutil.move( os.path.join( tmp_dir, filename ), os.path.join( output_extra_path, filename ) ) - out_html.write( '<li><a href="%s">%s</a></li>\n' % ( filename, filename ) ) - #out_html.write( '<li><a href="%s">%s</a>peakxls %s SomethingDifferent tmp_dir %s path %s exp_name %s</li>\n' % ( created_peak_xls_file, filename, filename, tmp_dir, output_extra_path, experiment_name ) ) - out_html.write( '</ul></p>\n' ) - out_html.write( '<h3>Messages from MACS:</h3>\n<p><pre>%s</pre></p>\n' % open( stderr_name, 'rb' ).read() ) - out_html.write( '</body></html>\n' ) - out_html.close() + # Convert XLS to interval, if requested + if output_xls_to_interval_peaks_file is not None: + peaks_xls_file = os.path.join(working_dir,'%s_peaks.xls' % experiment_name ) + if os.path.exists(peaks_xls_file): + convert_xls_to_interval(peaks_xls_file,output_xls_to_interval_peaks_file, + header='peaks file') + + # Move MACS2 output files from working dir to their final destinations + move_file(working_dir,"%s_summits.bed" % experiment_name,output_summits) + move_file(working_dir,"%s_peaks.xls" % experiment_name,output_peaks) + move_file(working_dir,"%s_peaks.narrowPeak" % experiment_name,output_narrowpeaks) + move_file(working_dir,"%s_peaks.broadPeak" % experiment_name,output_broadpeaks) + move_file(working_dir,"%s_peaks.gappedPeak" % experiment_name,output_gappedpeaks) + move_file(working_dir,"%s_treat_pileup.bdg" % experiment_name,output_treat_pileup) + move_file(working_dir,"%s_control_lambda.bdg" % experiment_name,output_lambda_bedgraph) + move_file(working_dir,"bdgcmp_out.bdg",output_bdgcmp) - #================================================================================= - #move files generated by bdgcmp command - if (options['command'] == "bdgcmp"): - created_bdgcmp_file = os.path.join (tmp_dir, "bdgcmp_out.bdg" ) - if os.path.exists( created_bdgcmp_file ): - shutil.move (created_bdgcmp_file, output_bdgcmp ) - - #================================================================================= - #cleanup - #================================================================================= - os.unlink( stderr_name ) - os.rmdir( tmp_dir ) + # Move remaining file to the 'extra files' path and link from the HTML + # file to allow user to access them from within Galaxy + html_file = open(output_extra_html,'wb') + html_file.write('<html><head><title>Additional output created by MACS (%s)</title></head><body><h3>Additional Files:</h3><p><ul>\n' % experiment_name) + # Make the 'extra files' directory + os.mkdir(output_extra_path) + # Move the files + for filen in sorted(os.listdir(working_dir)): + shutil.move(os.path.join(working_dir,filen), + os.path.join(output_extra_path,filen)) + html_file.write( '<li><a href="%s">%s</a></li>\n' % (filen,filen)) + # All files moved, close out HTML + html_file.write( '</ul></p>\n' ) + # Append any stderr output + html_file.write('<h3>Messages from MACS:</h3>\n<p><pre>%s</pre></p>\n' % + open(stderr_filen,'rb').read()) + html_file.write('</body></html>\n') + html_file.close() -if __name__ == "__main__": main() + # Clean up the working directory and files + os.unlink(stderr_filen) + os.rmdir(working_dir)
--- a/macs21_wrapper.xml Wed Jan 21 11:07:37 2015 -0500 +++ b/macs21_wrapper.xml Thu Jan 29 11:11:21 2015 -0500 @@ -1,25 +1,115 @@ -<tool id="fls_modencode_peakcalling_macs2.1" name="MACS2.1.0" version="2"> +<tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-1"> <requirements> <requirement type="package" version="2.7">python</requirement> <requirement type="package" version="1.8.1">numpy</requirement> <requirement type="package" version="2.1.0.20140616">macs2</requirement> </requirements> - <description>Model-based Analysis of ChIP-Seq [golem]</description> - <command interpreter="python">macs21_wrapper.py $options_file $outputs_file</command> + <description>Model-based Analysis of ChIP-Seq</description> + <command interpreter="python"> + macs21_wrapper.py + ## + ## Major command + $major_command.major_command_selector + ## + ## ChIP-seq input + $major_command.input_chipseq_file1 + ## + ## ChIP-seq control + #if str($major_command.input_control_file1) != 'None' + -c $major_command.input_control_file1 + #end if + ## + ## Call peaks + #if str($major_command.major_command_selector) == 'callpeak' + --format=$major_command.input_chipseq_file1.extension + --name="$experiment_name" + --bw=$major_command.bw + ## + ## Genome size + #if str($major_command.genome_size.gsize) == '' + --gsize=$major_command.genome_size.user_defined_gsize + #else: + --gsize=$major_command.genome_size.gsize + #end if + ## + ## Broad peaks + #if str($major_command.broad_options.broad_regions) == 'broad' + --broad --broad-cutoff=$major_command.broad_options.broad_cutoff + #end if + ## + ## (no)model options + #if str($major_command.nomodel_type.nomodel_type_selector) == 'nomodel' + --nomodel --extsize=$major_command.nomodel_type.extsize + #end if + ## + ## pq value select options + #if str($major_command.pq_options.pq_options_selector) == 'qvalue' + --qvalue=$major_command.pq_options.qvalue + #else + --pvalue=$major_command.pq_options.pvalue + #end if + ## + ## Advanced options + #if str($major_command.advanced_options.advanced_options_selector) == 'on' + --mfold $major_command.advanced_options.mfoldlo $major_command.advanced_options.mfoldhi + $major_command.advanced_options.nolambda + #if $major_command.bdg_options.bdg == True + -B $major_command.bdg_options.spmr + #end if + $major_command.advanced_options.call_summits + #if str($major_command.advanced_options.keep_duplicates.keep_dup) == '' + --keep-dup $major_command.advanced_options.keep_duplicates.maximum_tags + #else + --keep-dup $major_command.advanced_options.keep_duplicates.keep_dup + #end if + #else + ## Defaults if advanced options not set + --mfold 5 50 --keep-dup 1 + #end if + ## + ## Output files + --output-summits=$output_summits_bed_file + --output-extra-files=$output_extra_files + --output-extra-files-path=$output_extra_files.files_path + ## + ## Narrow/broad peak outputs + #if str($major_command.broad_options.broad_regions) == 'broad' + --output-broadpeaks=$output_broadpeaks_file + --output-gappedpeaks=$output_gappedpeaks_file + #else + --output-narrowpeaks=$output_narrowpeaks_file + #end if + ## + ## Bedgraph outputs + #if str($major_command.bdg_options.bdg) == 'True' + --output-pileup $output_treat_pileup_file + --output-lambda-bedgraph=$output_lambda_bedgraph_file + #end if + ## + ## XLS/interval output + #if str($major_command.xls_to_interval) == 'True' + --output-xls-to-interval=$output_xls_to_interval_peaks_file + #else + --output-peaks=$output_peaks_file + #end if + #end if + ## + ## Compare .bdg files + #if str($major_command.major_command_selector) == 'bdgcmp' + -m $major_command.bdgcmp_options.bdgcmp_options_selector + -p $major_command.pseudocount + --output-bdgcmp $output_bdgcmp_file + #end if + </command> <inputs> - <!--experiment name and option of selecting paired or single end will always be present--> + <!--experiment name used as base for output file names --> <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50" label="Experiment Name"/> - <!--select one of the 7 major commands offered by macs2--> + <!--select a major MACS2 command--> <conditional name="major_command"> <param name="major_command_selector" type="select" label="Select action to be performed"> <option value="callpeak">Peak Calling</option> - <!--<option value="filterdup">filterdup</option> - <option value="randsample">randsample</option>--> <option value="bdgcmp">Compare .bdg Files</option> - <!--<option value="bdgdiff">bdgdiff</option> - <option value="bdgpeakcall">bdgpeakcall</option> - <option value="bdgbroadcall">bdgbroadcall</option>--> </param> <!--callpeak option of macs2--> <when value="callpeak"> @@ -36,7 +126,6 @@ value="0.1" help="default: 0.1 (--broad-cutoff)"/> </when> </conditional> - <!--may need to add a few more formats at later time--> <param name="input_chipseq_file1" type="data" format="bed,sam,bam" label="ChIP-seq read file" /> <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True" @@ -217,123 +306,6 @@ <filter>major_command['major_command_selector'] == 'bdgcmp'</filter> </data> </outputs> - <configfiles> - <configfile name="outputs_file"><% -import simplejson -%> -##======================================================================================= -#set $__outputs = { 'command':str( $major_command.major_command_selector ) } -#if str( $major_command.major_command_selector ) == 'callpeak': - #set $__outputs['output_summits_bed_file'] = str( $output_summits_bed_file ) - #set $__outputs['output_extra_file'] = str( $output_extra_files ) - #set $__outputs['output_extra_file_path'] = str( $output_extra_files.files_path ) - #set $__outputs['output_peaks_file'] = str( $output_peaks_file ) - #set $__outputs['output_narrowpeaks_file'] = str( $output_narrowpeaks_file ) - #set $__outputs['output_broadpeaks_file'] = str( $output_broadpeaks_file ) - #set $__outputs['output_gappedpeaks_file'] = str( $output_gappedpeaks_file ) - #set $__outputs['output_xls_to_interval_peaks_file'] = str( $output_xls_to_interval_peaks_file ) - #set $__outputs['output_treat_pileup_file'] = str( $output_treat_pileup_file ) - #set $__outputs['output_lambda_bedgraph_file'] = str( $output_lambda_bedgraph_file ) -#end if -##======================================================================================= -#if str( $major_command.major_command_selector ) == 'bdgcmp': - #set $__outputs['output_bdgcmp_file'] = str( $output_bdgcmp_file ) -#end if - -${ simplejson.dumps( __outputs ) } - </configfile> - <configfile name="options_file"><% -import simplejson -%> -##======================================================================================= -#set $__options = { 'experiment_name':str( $experiment_name ) } -##treatment/tag input files and format -#set $__options['input_chipseq'] = [ str( $major_command.input_chipseq_file1 ) ] -#set $__options['format'] = $major_command.input_chipseq_file1.extension.upper() - -##control/input files -#set $__options['input_control'] = [] -#if str( $major_command.input_control_file1 ) != 'None': - #set $_hole = __options['input_control'].append( str( $major_command.input_control_file1 ) ) -#end if - -#if str( $major_command.major_command_selector ) == 'callpeak': - #set $__options['command'] = str( "callpeak" ) - #set $__options['bw'] = str( $major_command.bw ) - #set $__options['xls_to_interval'] = str( $major_command.xls_to_interval ) - - ##bdg options - #if $major_command.bdg_options.bdg == True: - #set $__options['bdg'] = str( "-B" ) - #set $__options['spmr'] = str( $major_command.bdg_options.spmr ) - #else: - #set $__options['bdg'] = str( "" ) - #set $__options['spmr'] = str( "" ) - #end if - - ##broad_options - #if str( $major_command.broad_options.broad_regions ) == 'broad': - #set $__options['broad'] = str( $major_command.broad_options.broad_regions ) - #set $__options['broad_cutoff'] = str( $major_command.broad_options.broad_cutoff ) - #else: - #set $__options['broad'] = str( "" ) - #set $__options['broad_cutoff'] = str( "" ) - #end if - - ##genome sizes - #if str( $major_command.genome_size.gsize ) == '': - #set $__options['gsize'] = int( $major_command.genome_size.user_defined_gsize ) - #else: - #set $__options['gsize'] = str( $major_command.genome_size.gsize ) - #end if - - ##advanced options - #if str( $major_command.advanced_options.advanced_options_selector ) == 'on': - #set $__options['mfoldlo'] = int( $major_command.advanced_options.mfoldlo ) - #set $__options['mfoldhi'] = int( $major_command.advanced_options.mfoldhi ) - #set $__options['nolambda'] = str( $major_command.advanced_options.nolambda ) - #set $__options['call_summits'] = str( $major_command.advanced_options.call_summits ) - #if str( $major_command.advanced_options.keep_duplicates.keep_dup ) == '': - #set $__options['keep_dup'] = int( $major_command.advanced_options.keep_duplicates.maximum_tags ) - #else: - #set $__options['keep_dup'] = str( $major_command.advanced_options.keep_duplicates.keep_dup ) - #end if - #else: - #set $__options['mfoldlo'] = int( "5" ) - #set $__options['mfoldhi'] = int( "50" ) - #set $__options['nolambda'] = str( "" ) - #set $__options['call_summits'] = str( "" ) - #set $__options['keep_dup'] = int( "1" ) - #end if - - ##enable xls file options - ##if str( $major_command.xls_to_interval ) == 'create': - ##set $__options['xls_to_interval'] = { 'peaks_file': str( $output_xls_to_interval_peaks_file ), 'negative_peaks_file': str( $output_xls_to_interval_negative_peaks_file ) } - ##end if - - ##pq value select options - #if str( $major_command.pq_options.pq_options_selector ) == 'qvalue': - #set $__options['qvalue'] = str( $major_command.pq_options.qvalue ) - #else: - #set $__options['pvalue'] = str( $major_command.pq_options.pvalue ) - #end if - - ##model options - #if str( $major_command.nomodel_type.nomodel_type_selector ) == 'nomodel': - #set $__options['nomodel'] = str( $major_command.nomodel_type.extsize ) - #end if -#end if -##======================================================================================= -#if str( $major_command.major_command_selector ) == 'bdgcmp': - #set $__options['command'] = str( "bdgcmp" ) - #set $__options['pseudocount'] = float( str( $major_command.pseudocount ) ) - #set $__options['m'] = str( $major_command.bdgcmp_options.bdgcmp_options_selector ) -#end if -##======================================================================================= - -${ simplejson.dumps( __options ) } - </configfile> - </configfiles> <tests> <!--none yet for macs2--> </tests>
--- a/tool_dependencies.xml Wed Jan 21 11:07:37 2015 -0500 +++ b/tool_dependencies.xml Thu Jan 29 11:11:21 2015 -0500 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="python" version="2.7"> - <repository changeset_revision="74d009a2a4cb" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="2c52c900e56a" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="numpy" version="1.8.1"> <repository changeset_revision="0f9f634dec8a" name="package_numpy_1_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> @@ -11,7 +11,7 @@ <actions> <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action> <action type="set_environment_for_install"> - <repository changeset_revision="74d009a2a4cb" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="2c52c900e56a" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="python" version="2.7" /> </repository> <repository changeset_revision="0f9f634dec8a" name="package_numpy_1_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">