# HG changeset patch
# User nikos
# Date 1405423179 14400
# Node ID 998c98233c36b917251b016c91ed3a856ffc4047
# Parent  5b5460b79488ff9bacb38ba691dfe2ffd210d874
Uploaded

diff -r 5b5460b79488 -r 998c98233c36 bigWigSummary.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bigWigSummary.xml	Tue Jul 15 07:19:39 2014 -0400
@@ -0,0 +1,33 @@
+<tool id="bigWigSummary" name="bigWigSummary">
+  <description> Extract summary information from a bigWig file. </description>
+  <command> 
+	bigWigSummary $input $chrom $start $end $dataPoints -type=$type> $output
+  </command>
+  <inputs>
+    <param name="input" type="data" format="bigwig" label="Input"/>
+    <param name="chrom" type="text" value="chr" label="Chromosome" help="E.g. 'chr7'"/>
+    <param name="start" type="integer" value="" label="Start coordinate" help="BED format (0-based)."/>
+    <param name="end" type="integer" value="" label="End coordinate" help="BED format (0-based)."/>    
+      
+    <param name="dataPoints" type="integer" value="1" label="Number of (equal) parts to break down the selected region."  help="Choose 1 for simple summary."/>
+    <param name="type" type="select" label="Operation">
+	<option value="mean">Average value in region (default)</option>
+        <option value="min">Minimum value in region</option>
+        <option value="max">Maximum value in region</option>
+        <option value="std">Standard deviation in region</option>
+        <option value="coverage">Percentage of region that is covered</option>
+    </param>
+  </inputs>
+  
+  <outputs>
+    <data format="text" name="output"/> 
+  </outputs>
+  <help>
+
+**Usage**
+  * bigWigSummary file.bigWig chrom start end dataPoints
+  * Get summary data from bigWig for indicated region, broken into dataPoints equal parts.  (Use dataPoints=1 for simple summary.)
+
+  </help>
+</tool>
+