--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/IntervalLengthDistribution.xml	Tue Jun 19 22:15:09 2012 -0400
@@ -0,0 +1,38 @@
+<tool id="IntervalLengthDistribution" name="Make histogram" version="1.0.0">
+  <description>of read lengths</description>
+  <command interpreter="sh">galaxyToolRunner.sh ngs.IntervalLengthDistribution -i $input $freq -o $output</command>
+  <inputs>
+      <param name="input" type="data" format="sam,bam,bed,bedgraph,gff" label="Reads/Intervals" />
+      <param name="freq" type="boolean" checked="false" truevalue="-f" falsevalue="" label="Output normalized frequencies rather than counts" />
+  </inputs>
+  <outputs>
+      <data format="tabular" name="output" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="test.bed"/>
+      <param name="freq" value="false"/>
+	    <output name="output" file="intervallengthdistribution1.txt"/>
+    </test>
+    <test>
+      <param name="input" value="test.bed"/>
+      <param name="freq" value="true"/>
+	    <output name="output" file="intervallengthdistribution2.txt"/>
+    </test>
+    <test>
+      <param name="input" value="test2.bed"/>
+      <param name="freq" value="false"/>
+	    <output name="output" file="intervallengthdistribution3.txt"/>
+    </test>
+  </tests>
+  
+<help>
+  
+This tool calculates the distribution of interval lengths from a list of intervals or reads in SAM, BAM, Bed, BedGraph, or GFF format.
+
+.. class:: warningmark
+
+For paired-end sequencing reads, the length is the length of the fragment (5' end of read 1 to 5' end of read 2)
+
+</help>
+</tool>