diff bigWigSummary.xml @ 20:3dede45026d7 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bigWigSummary.xml	Tue Sep 09 10:32:57 2014 -0400
@@ -0,0 +1,43 @@
+<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>
+
+    <tests>
+	<test>
+	    <param name="input" value="1.bigwig" />
+	    <param name="chrom" value="chr21" />
+	    <param name="start" value="10000000" />
+            <param name="end" value="50000000" />
+	    <param name="dataPoints" value="3" />
+	    <param name="type" value="std" />
+	    <output name="output" value="1.txt" />
+	</test>
+    </tests>
+    <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>