diff clusterBed.xml @ 8:0d3aa592ce27 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clusterBed.xml	Tue Apr 28 22:56:34 2015 -0400
@@ -0,0 +1,50 @@
+<tool id="bedtools_clusterbed" name="ClusterBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        bedtools cluster
+        $strand
+        -d $distance
+        -i $inputA
+        > $output
+]]>
+    </command>
+    <inputs>
+        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
+        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness." 
+            help="That is, only cluster features that are the same strand. By default, this is disabled." />
+        <param name="distance" type="integer" value="0" 
+            label="Maximum distance between features allowed for features to be clustered" 
+            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"/>
+    </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.
+
+.. image:: $PATH_TO_IMAGES/cluster-glyph.png
+
+.. class:: warningmark
+
+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>