--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_wrapper.xml	Fri Jan 18 09:47:43 2013 -0500
@@ -0,0 +1,233 @@
+<tool id="modencode_peakcalling_macs2" name="MACS2" version="2.0.10.2">
+  <description>Model-based Analysis of ChIP-Seq</description>
+  <!--<command interpreter="python">macs2_wrapper.py $options_file $output_bed_file $output_extra_files $output_extra_files.files_path $output_peaks_file $output_narrowpeaks_file</command>-->
+  <command interpreter="python">macs2_wrapper.py $options_file $outputs_file</command>
+  <requirements>
+    <requirement type="python-module">macs2</requirement>
+    <requirement type="package">macs2</requirement>
+  </requirements>
+  <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>