# HG changeset patch
# User modencode-dcc
# Date 1358543274 18000
# Node ID 25494d2324333ab7f18c5f15e54863f7f7c7a44c
# Parent  522a47128d55cb048b95e374d69373cbd7e5bd5a
Deleted selected files

diff -r 522a47128d55 -r 25494d232433 macs2_wrapper.xml
--- a/macs2_wrapper.xml	Fri Jan 18 14:31:35 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,233 +0,0 @@
-<tool id="modencode_peakcalling_macs2" name="MACS2" version="2.0.10.2">
-  <requirements>
-    <requirement type="python-module">macs2</requirement>
-    <requirement type="package" version="2.0.10.2">macs2</requirement>
-    <!--<requirement type="set_environment">SCRIPT_PATH</requirement>-->
-  </requirements>
-  <description>Model-based Analysis of ChIP-Seq</description>
-  <command interpreter="python">macs2_wrapper.py $options_file $outputs_file</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"/>
-    
-    <!--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>-->
-      </param>
-      <!--callpeak option of macs2-->
-      <when value="callpeak">
-	<!--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"/>
-
-	<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="nomodel_type_selector" type="select" label="Build Model">
-	   <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">
-            <param name="shiftsize" type="integer" label="Arbitrary shift size in bp" value="100" help="(--shiftsize)"/>
-          </when>
-        </conditional>
-      </when>
-
-      <!--callpeak option of macs2-->
-      <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)"/>
-
-        <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>
-          </param>
-	</conditional>
-      </when>
-    </conditional>
-  </inputs>
-
-  <outputs>
-    <!--callpeaks output-->
-    <data name="output_bed_file" format="bed" label="${tool.name}: callpeak on ${on_string} (peaks: bed)">
-      <filter>major_command['major_command_selector'] == 'callpeak'</filter>
-    </data>
-    <data name="output_extra_files" format="html" label="${tool.name}: callpeak on ${on_string} (html report)">
-      <filter>major_command['major_command_selector'] == 'callpeak'</filter>
-    </data>
-    <data name="output_peaks_file" format="xls" label="${tool.name}: callpeak on ${on_string} (peaks: xls)">
-      <filter>major_command['major_command_selector'] == 'callpeak'</filter>
-    </data>
-    <data name="output_narrowpeaks_file" format="txt" label="${tool.name}: callpeak on ${on_string} (peaks: encodePeak)">
-      <filter>major_command['major_command_selector'] == 'callpeak'</filter>
-    </data>
-    <data name="output_xls_to_interval_peaks_file" format="interval" label="${tool.name}: callpeak on ${on_string} (peaks: interval)">
-      <filter>major_command['xls_to_interval'] is True</filter>
-      <filter>major_command['major_command_selector'] == 'callpeak'</filter>
-    </data>
-    <data name="output_xls_to_interval_negative_peaks_file" format="interval" label="${tool.name}: callpeak on ${on_string} (negative peaks: interval)">
-      <filter>major_command['xls_to_interval'] is True</filter>
-      <filter>major_command['input_control_file1'] is not None</filter>
-      <filter>major_command['major_command_selector'] == 'callpeak'</filter>
-    </data>
-    <!--bdgcmp output-->
-    <data name="output_bdgcmp_file" format="bdg" label="${tool.name}: bdgcmp on ${on_string} (bdg)">
-      <filter>major_command['major_command_selector'] == 'bdgcmp'</filter>
-    </data>
-  </outputs>
-  <configfiles>
-
-    <configfile name="outputs_file">&lt;%
-import simplejson
-%&gt;
-##=======================================================================================
-#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 )
-#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">&lt;%
-import simplejson
-%&gt;
-##=======================================================================================
-#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['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
-
-	##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( $major_command.bdgcmp_options.bdgcmp_options_selector )
-#end if
-##=======================================================================================
-
-${ simplejson.dumps( __options ) }
-    </configfile>
-  </configfiles>
-  <tests>
-	<!--none yet for macs2-->
-  </tests>
-  <help>
-**What it does**
-
-With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq)
-is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for
-identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of
-binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.
-
-View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README
-
-------
-
-**Usage**
-
-**Peak Calling**: Main MACS2 Function to Call peaks from alignment results.
-
-**Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph.
-
-
-------
-
-**Citation**
-
-For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
-
-Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
-  </help>
-</tool>
\ No newline at end of file