Mercurial > repos > stemcellcommons > macs2
changeset 1:c05f607d116c draft default tip
Replace simplejson with json. Add option to call broad peaks.
| author | stemcellcommons |
|---|---|
| date | Tue, 20 May 2014 12:10:38 -0400 |
| parents | 642c0da30ca6 |
| children | |
| files | macs2_wrapper.py macs2_wrapper.xml |
| diffstat | 2 files changed, 180 insertions(+), 166 deletions(-) [+] |
line wrap: on
line diff
--- a/macs2_wrapper.py Thu Oct 17 12:47:49 2013 -0400 +++ b/macs2_wrapper.py Tue May 20 12:10:38 2014 -0400 @@ -1,12 +1,9 @@ -#purpose: macs2 python wrapper -#author: Ziru Zhou -#date: November, 2012 +# macs2 python wrapper +# based on 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 json CHUNK_SIZE = 1024 @@ -38,12 +35,12 @@ #keep all existing comment lines if line.startswith( '#' ): out.write( line ) - #added for macs2 since there is an extra newline + #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 + print line wrote_header = True else: fields = line.split( '\t' ) @@ -57,8 +54,8 @@ #========================================================================================== def main(): #take in options file and output file names - options = simplejson.load( open( sys.argv[1] ) ) - outputs = simplejson.load( open( sys.argv[2] ) ) + options = json.load( open( sys.argv[1] ) ) + outputs = json.load( open( sys.argv[2] ) ) #================================================================================= #parse options and execute macs2 @@ -71,26 +68,29 @@ #================================================================================= if (options['command'] == "callpeak"): - output_bed = outputs['output_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_xls_to_interval_peaks_file = outputs['output_xls_to_interval_peaks_file'] - output_xls_to_interval_negative_peaks_file = outputs['output_xls_to_interval_negative_peaks_file'] + output_bed = outputs['output_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_xls_to_interval_peaks_file = outputs['output_xls_to_interval_peaks_file'] + output_xls_to_interval_negative_peaks_file = outputs['output_xls_to_interval_negative_peaks_file'] - if 'pvalue' in options: - cmdline = "%s --format='%s' --name='%s' --gsize='%s' --bw='%s' --pvalue='%s' --mfold %s %s %s %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['bw'], options['pvalue'], options['mfoldlo'], options['mfoldhi'], options['nolambda'], options['bdg'] ) - elif 'qvalue' in options: - cmdline = "%s --format='%s' --name='%s' --gsize='%s' --bw='%s' --qvalue='%s' --mfold %s %s %s %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['bw'], options['qvalue'], options['mfoldlo'], options['mfoldhi'], options['nolambda'], options['bdg'] ) - - if 'nomodel' in options: - cmdline = "%s --nomodel --shiftsize='%s'" % ( cmdline, options['nomodel'] ) + if 'pvalue' in options: + cmdline = "%s --format='%s' --name='%s' --gsize='%s' --bw='%s' --pvalue='%s' --mfold %s %s %s %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['bw'], options['pvalue'], options['mfoldlo'], options['mfoldhi'], options['nolambda'], options['bdg'] ) + elif 'qvalue' in options: + cmdline = "%s --format='%s' --name='%s' --gsize='%s' --bw='%s' --qvalue='%s' --mfold %s %s %s %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['bw'], options['qvalue'], options['mfoldlo'], options['mfoldhi'], options['nolambda'], options['bdg'] ) + + if 'broad_cutoff' in options: + cmdline += " --broad --broad-cutoff=%s" % (options['broad_cutoff']) + + if 'nomodel' in options: + cmdline = "%s --nomodel --shiftsize='%s'" % ( cmdline, options['nomodel'] ) #================================================================================= if (options['command'] == "bdgcmp"): - output_bdgcmp = outputs['output_bdgcmp_file'] + output_bdgcmp = outputs['output_bdgcmp_file'] - cmdline = "%s -m %s -p %s -o bdgcmp_out.bdg" % ( cmdline, options['m'], options['pseudocount'] ) + cmdline = "%s -m %s -p %s -o bdgcmp_out.bdg" % ( cmdline, options['m'], options['pseudocount'] ) #================================================================================= tmp_dir = tempfile.mkdtemp() #macs makes very messy output, need to contain it into a temp dir, then provide to user @@ -115,59 +115,59 @@ #================================================================================= #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() + #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_peaks.bed" % experiment_name ) - if os.path.exists( created_bed_name ): - shutil.move( created_bed_name, output_bed ) + #move bed out to proper output file + created_bed_name = os.path.join( tmp_dir, "%s_peaks.bed" % experiment_name ) + if os.path.exists( created_bed_name ): + shutil.move( created_bed_name, output_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 ) + #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.encodePeak" % experiment_name ) - if os.path.exists( created_narrowpeak_file ): - shutil.move (created_narrowpeak_file, output_narrowpeaks ) + #peaks.encodepeaks (narrowpeaks) file + created_narrowpeak_file = os.path.join (tmp_dir, "%s_peaks.encodePeak" % experiment_name ) + if os.path.exists( created_narrowpeak_file ): + shutil.move (created_narrowpeak_file, output_narrowpeaks ) - #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' ) - create_peak_xls_file = os.path.join( tmp_dir, '%s_negative_peaks.xls' % experiment_name ) - if os.path.exists( create_peak_xls_file ): - print "negative file exists" - xls_to_interval( create_peak_xls_file, output_xls_to_interval_negative_peaks_file, header = 'negative peaks file' ) + #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' ) + create_peak_xls_file = os.path.join( tmp_dir, '%s_negative_peaks.xls' % experiment_name ) + if os.path.exists( create_peak_xls_file ): + print "negative file exists" + xls_to_interval( create_peak_xls_file, output_xls_to_interval_negative_peaks_file, header = 'negative peaks file' ) - #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() + #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() #================================================================================= #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 ) - + 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 #=================================================================================
--- a/macs2_wrapper.xml Thu Oct 17 12:47:49 2013 -0400 +++ b/macs2_wrapper.xml Tue May 20 12:10:38 2014 -0400 @@ -1,6 +1,7 @@ <tool id="macs2_peakcalling" name="MACS2" version="2.0.10"> <description>Model-based Analysis of ChIP-Seq</description> <command interpreter="python">macs2_wrapper.py $options_file $outputs_file</command> + <version_command>macs2 --version</version_command> <inputs> <!--experiment name and option of selecting paired or single end will always be present--> <param name="experiment_name" type="text" value="MACS2 in Galaxy" size="50" label="Experiment Name"/> @@ -8,53 +9,63 @@ <!--select one of the 7 major commands offered by macs2--> <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>--> + <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"> - <!--may need to add a few more formats at later time--> + <!--may need to add a few more formats at later time--> <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" /> <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" /> - <param name="gsize" type="float" label="Effective genome size" value="2.7e+9" help="Human: 3.3e+9, Mouse: 3.0e+9, Fly: 1.9e+8, Worm: 1.3e+8 (--gsize)"/> - <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/> - <param name="xls_to_interval" label="Parse xls files into into distinct interval files" type="boolean" truevalue="True" falsevalue="False" checked="False"/> - <param name="bdg" label="Save fragment pileup, control lambda, -log10pvalue/qvalue in bedGraph" type="boolean" truevalue="-B" falsevalue="" checked="False" help="files located in html report"/> + <param name="gsize" type="float" label="Effective genome size" value="2.7e+9" help="Human: 3.3e+9, Mouse: 3.0e+9, Fly: 1.9e+8, Worm: 1.3e+8 (--gsize)"/> + <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/> + <param name="xls_to_interval" label="Parse xls files into into distinct interval files" type="boolean" truevalue="True" falsevalue="False" checked="False"/> + <param name="bdg" label="Save fragment pileup, control lambda, -log10pvalue/qvalue in bedGraph" type="boolean" truevalue="-B" falsevalue="" checked="False" help="files located in html report"/> - <conditional name="pq_options"> - <param name="pq_options_selector" type="select" label="Select p-value or q-value" help="default uses q-value"> - <option value="qvalue">q-value</option> - <option value="pvalue">p-value</option> - </param> - <when value="pvalue"> - <param name="pvalue" type="float" label="p-value cutoff for peak detection" value="1e-2" help="default: 1e-2 (--pvalue)"/> - </when> - <when value="qvalue"> - <param name="qvalue" type="float" label="q-value cutoff for peak detection" value="5e-2" help="default: 5e-2 (--qvalue)"/> - </when> - </conditional> - <conditional name="advanced_options"> - <param name="advanced_options_selector" type="select" label="Display advanced options"> - <option value="off">Hide</option> - <option value="on">Display</option> - </param> - <when value="on"> + <conditional name="pq_options"> + <param name="pq_options_selector" type="select" label="Select p-value or q-value" help="default uses q-value"> + <option value="qvalue">q-value</option> + <option value="pvalue">p-value</option> + </param> + <when value="pvalue"> + <param name="pvalue" type="float" label="p-value cutoff for peak detection" value="1e-2" help="default: 1e-2 (--pvalue)"/> + </when> + <when value="qvalue"> + <param name="qvalue" type="float" label="q-value cutoff for peak detection" value="5e-2" help="default: 5e-2 (--qvalue)"/> + </when> + </conditional> + <conditional name="advanced_options"> + <param name="advanced_options_selector" type="select" label="Display advanced options"> + <option value="off">Hide</option> + <option value="on">Display</option> + </param> + <when value="on"> <param name="mfoldlo" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (lower-limit)" value="10" help="(--mfold)"/> - <param name="mfoldhi" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (upper-limit)" value="30" help="(--mfold)"/> - <param name="nolambda" label="Use fixed background lambda as local lambda for every peak region" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" help="up to 9X more time consuming (--nolambda)"/> - </when> - <when value="off"> - <!--display nothing--> - </when> - </conditional> - <conditional name="nomodel_type"> + <param name="mfoldhi" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (upper-limit)" value="30" help="(--mfold)"/> + <param name="nolambda" label="Use fixed background lambda as local lambda for every peak region" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" help="up to 9X more time consuming (--nolambda)"/> + <conditional name="broad_options"> + <param name="broad_options_selector" type="select" label="Composite broad regions" help="put nearby highly enriched regions into a broad region with loose cutoff (--broad)"> + <option value="nobroad" selected="true">No broad regions</option> + <option value="broad">Broad regions</option> + </param> + <when value="broad"> + <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1" help="value is either p-value or q-value as specified above (--broad-cutoff)"/> + </when> + <when value="nobroad"/> + </conditional> + </when> + <when value="off"> + <!--display nothing--> + </when> + </conditional> + <conditional name="nomodel_type"> <param name="nomodel_type_selector" type="select" label="Build Model"> - <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option> + <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option> <option value="create_model" selected="true">Build the shifting model (--nomodel disabled)</option> </param> <when value="nomodel"> @@ -67,18 +78,18 @@ <when value="bdgcmp"> <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" /> <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" /> - <param name="pseudocount" type="float" label="Set pseudocount" value="0.00001" help="default: 0.00001 (-p)"/> + <param name="pseudocount" type="float" label="Set pseudocount" value="0.00001" help="default: 0.00001 (-p)"/> <conditional name="bdgcmp_options"> <param name="bdgcmp_options_selector" type="select" label="Select action to be performed"> - <option value="ppois">ppois</option> - <option value="qpois">qpois</option> - <option value="subtract">subtract</option> - <option value="logFE">logFE</option> - <option value="FE">FE</option> - <option value="logLR">logLR</option> + <option value="ppois">ppois</option> + <option value="qpois">qpois</option> + <option value="subtract">subtract</option> + <option value="logFE">logFE</option> + <option value="FE">FE</option> + <option value="logLR">logLR</option> </param> - </conditional> + </conditional> </when> </conditional> </inputs> @@ -114,28 +125,28 @@ <configfiles> <configfile name="outputs_file"><% -import simplejson +import json %> ##======================================================================================= #set $__outputs = { 'command':str( $major_command.major_command_selector ) } #if str( $major_command.major_command_selector ) == 'callpeak': - #set $__outputs['output_bed_file'] = str( $output_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_xls_to_interval_peaks_file'] = str( $output_xls_to_interval_peaks_file ) - #set $__outputs['output_xls_to_interval_negative_peaks_file'] = str( $output_xls_to_interval_negative_peaks_file ) + #set $__outputs['output_bed_file'] = str( $output_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_xls_to_interval_peaks_file'] = str( $output_xls_to_interval_peaks_file ) + #set $__outputs['output_xls_to_interval_negative_peaks_file'] = str( $output_xls_to_interval_negative_peaks_file ) #end if ##======================================================================================= #if str( $major_command.major_command_selector ) == 'bdgcmp': - #set $__outputs['output_bdgcmp_file'] = str( $output_bdgcmp_file ) + #set $__outputs['output_bdgcmp_file'] = str( $output_bdgcmp_file ) #end if -${ simplejson.dumps( __outputs ) } +${ json.dumps( __outputs ) } </configfile> <configfile name="options_file"><% -import simplejson +import json %> ##======================================================================================= #set $__options = { 'experiment_name':str( $experiment_name ) } @@ -146,57 +157,60 @@ ##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 ) ) + #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['gsize'] = int( $major_command.gsize ) - #set $__options['bw'] = str( $major_command.bw ) - #set $__options['bdg'] = str( $major_command.bdg ) - #set $__options['xls_to_interval'] = str( $major_command.xls_to_interval ) - - ##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 ) - #else: - #set $__options['mfoldlo'] = int( "10" ) - #set $__options['mfoldhi'] = int( "30" ) - #set $__options['nolambda'] = str( "" ) - #end if + #set $__options['command'] = str( "callpeak" ) + #set $__options['gsize'] = int( $major_command.gsize ) + #set $__options['bw'] = str( $major_command.bw ) + #set $__options['bdg'] = str( $major_command.bdg ) + #set $__options['xls_to_interval'] = str( $major_command.xls_to_interval ) - ##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.shiftsize ) - #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( $major_command.advanced_options.nolambda ) + #if str($major_command.advanced_options.broad_options.broad_options_selector) == 'broad' + #set $__options['broad_cutoff'] = str($major_command.advanced_options.broad_options.broad_cutoff) + #end if + #else: + #set $__options['mfoldlo'] = int( "10" ) + #set $__options['mfoldhi'] = int( "30" ) + #set $__options['nolambda'] = str( "" ) + #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.shiftsize ) + #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 ) + #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 ) } +${ json.dumps( __options ) } </configfile> </configfiles> <tests> - <!--none yet for macs2--> + <!--none yet for macs2--> </tests> <help> **What it does**