diff clusterBed.xml @ 1:82aac94b06c3 draft

Uploaded

--- a/clusterBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/clusterBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,11 +6,13 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
+<![CDATA[
         bedtools cluster
         $strand
         -d $distance
         -i $inputA
-        &gt; $output
+        > $output
+]]>
     </command>
     <inputs>
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
@@ -21,10 +23,16 @@
             help="Default is 0. That is, overlapping and/or book-ended features are clustered." />
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
+        <data format_source="inputA" name="output" metadata_source="inputA"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="inputA" value="mergedBed1.bed" ftype="bed" />
+            <output name="output" file="clusterBed_result.bed" ftype="bed" />
+        </test>
+    </tests>
     <help>
-
+<![CDATA[
 **What it does**
 
 Similar to merge, cluster report each set of overlapping or “book-ended” features in an interval file. In contrast to merge, cluster does not flatten the cluster of intervals into a new meta-interval; instead, it assigns an unique cluster ID to each record in each cluster. This is useful for having fine control over how sets of overlapping intervals in a single interval file are combined.
@@ -36,6 +44,7 @@
 bedtools cluster requires that you presort your data by chromosome and then by start position (e.g., sort -k1,1 -k2,2n in.bed > in.sorted.bed for BED files).
 
 @REFERENCES@
+]]>
     </help>
     <expand macro="citations" />
 </tool>