Mercurial > repos > iuc > bedtools
comparison clusterBed.xml @ 0:4fb5ea02b441 draft
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| author | iuc |
|---|---|
| date | Tue, 15 Jul 2014 14:42:23 -0400 |
| parents | |
| children | 7511823bdea1 |
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| -1:000000000000 | 0:4fb5ea02b441 |
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| 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 </tool> |