|
0
|
1 <tool id="bedtools_clusterbed" name="ClusterBed" version="@WRAPPER_VERSION@.0">
|
|
|
2 <description></description>
|
|
|
3 <macros>
|
|
|
4 <import>macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <expand macro="requirements" />
|
|
|
7 <expand macro="stdio" />
|
|
|
8 <command>
|
|
|
9 bedtools cluster
|
|
|
10 $strand
|
|
|
11 -d $distance
|
|
|
12 -i $inputA
|
|
|
13 > $output
|
|
|
14 </command>
|
|
|
15 <inputs>
|
|
|
16 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
|
|
|
17 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness."
|
|
|
18 help="That is, only cluster features that are the same strand. By default, this is disabled." />
|
|
|
19 <param name="distance" type="integer" value="0"
|
|
|
20 label="Maximum distance between features allowed for features to be clustered"
|
|
|
21 help="Default is 0. That is, overlapping and/or book-ended features are clustered." />
|
|
|
22 </inputs>
|
|
|
23 <outputs>
|
|
|
24 <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
|
|
|
25 </outputs>
|
|
|
26 <help>
|
|
|
27
|
|
|
28 **What it does**
|
|
|
29
|
|
|
30 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.
|
|
|
31
|
|
|
32 .. image:: $PATH_TO_IMAGES/cluster-glyph.png
|
|
|
33
|
|
|
34 .. class:: warningmark
|
|
|
35
|
|
|
36 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).
|
|
|
37
|
|
|
38 @REFERENCES@
|
|
|
39 </help>
|
|
|
40 <expand macro="citations" />
|
|
|
41 </tool>
|
