# HG changeset patch
# User jbrayet
# Date 1455025395 18000
# Node ID 5ee836825323485a2327f9c427034d5afef80af2
# Parent  77a6b67de66d0d0022f01e78b094121cb697e702
Uploaded

diff -r 77a6b67de66d -r 5ee836825323 FilterPeaks.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FilterPeaks.xml	Tue Feb 09 08:43:15 2016 -0500
@@ -0,0 +1,68 @@
+<tool id="filterControl" name="Filter Peaks" version="1.0">
+  <description>Filter FindPeaks output (.peaks) using Control Peaks</description>
+  <requirements>
+    <container type="docker">institutcuriengsintegration/filterpeaks:1.0</container>
+  </requirements>
+  <command interpreter="bash">
+  FilterPeaks.sh -f $inputfile -c $controlfile -t $minHeight -v $minRatio -m $minHeightControl -r ${__root_dir__}
+  
+  #if $if_bed.if_bed_selector == "yes"
+    -o $outputB
+    -w $outputBC
+    -b $if_bed.if_bed_selector
+    -q $if_bed.nameControl
+    -n $if_bed.nameChIP
+    -l $if_bed.genome_selector
+  #else
+    -o $output
+    -w $outputC
+  #end if
+ </command>
+   <inputs>
+   
+    <param name="inputfile" type="data" label="ChIP: File with peaks" value="ChIP-Seq File" format="txt"/>
+    <param name="controlfile" type="data" label="Control: File with peaks" value="Control File" format="txt"/>
+    <param name="minHeight" type="integer" label="Minimal peak height to consider for the ChIP dataset" value="8"/>
+    <param name="minHeightControl" type="integer" label="Minimal peak height to consider for the Control dataset" value="4"/>
+    <param name="minRatio" type="float" label="Minimal ratio ChIP/Control" value="1.6"/>
+
+   <conditional name="if_bed">
+    <param name="if_bed_selector" type="select" label="Do you want the output in .BED format" help="By default the output will be in .PEAKS format of FindPeaks">
+        <option value="no" selected="true">No</option>
+        <option value="yes">Yes</option>
+    </param>
+    <when value="yes">
+    <param name="genome_selector" type="select" label="Select the genome under study">
+        <option value="hg19" selected="true">hg19</option>	
+        <option value="hg18">hg18</option>
+        <option value="mm9">mm9</option>   
+        <option value="mm10">mm10</option>    
+    </param>
+    <param name="nameChIP" type="text" label="header for ChIP .bed file" value="ChIP_name"/>
+    <param name="nameControl" type="text" label="header for Control .bed file" value="Control_name"/>
+    </when>    
+    </conditional>
+
+
+  </inputs>
+  <outputs>
+    <data name="output" format="txt" label="filtered peaks for ChIP (.peaks)">
+      <filter>(if_bed['if_bed_selector'] == 'no')</filter>
+    </data>   
+    <data name="outputC" format="txt" label="filtered peaks for Control (.peaks)">
+      <filter>(if_bed['if_bed_selector'] == 'no')</filter>
+    </data>
+    <data name="outputB" format="bed" label="filtered peaks for ChIP (.bed)">   
+       <filter>(if_bed['if_bed_selector'] == 'yes')</filter>
+    </data>
+    <data name="outputBC" format="bed" label="filtered peaks for Control (.bed)">   
+       <filter>(if_bed['if_bed_selector'] == 'yes')</filter>
+    </data>
+  </outputs>
+  <help>
+**What it does**
+
+Filters out peaks present both in ChIP and Control dataset
+
+  </help>
+</tool>