Mercurial > repos > stemcellcommons > macs2

changeset 21:eed6c8dcef5d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add option to call broad peaks.
author stemcellcommons
date Wed, 16 Apr 2014 15:30:35 -0400
parents db2805f9df66
children
files macs2_wrapper.py macs2_wrapper.xml
diffstat 2 files changed, 171 insertions(+), 154 deletions(-) [+]
line wrap: on
line diff
--- a/macs2_wrapper.py	Wed Apr 09 18:06:03 2014 -0400
+++ b/macs2_wrapper.py	Wed Apr 16 15:30:35 2014 -0400
@@ -35,12 +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' )
@@ -68,26 +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
@@ -112,59 +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	Wed Apr 09 18:06:03 2014 -0400
+++ b/macs2_wrapper.xml	Wed Apr 16 15:30:35 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>
@@ -119,17 +130,17 @@
 ##=======================================================================================
 #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
 
 ${ json.dumps( __outputs ) }
@@ -146,49 +157,52 @@
 ##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
 ##=======================================================================================
 
@@ -196,7 +210,7 @@
     </configfile>
   </configfiles>
   <tests>
-	<!--none yet for macs2-->
+        <!--none yet for macs2-->
   </tests>
   <help>
 **What it does**