Mercurial > repos > stemcellcommons > macs2
diff macs2_wrapper.xml @ 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 |
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--- 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**