Mercurial > repos > iuc > bedtools
comparison clusterBed.xml @ 10:71af3ebbbb7a draft
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| author | iuc |
|---|---|
| date | Wed, 29 Apr 2015 12:06:53 -0400 |
| parents | 0d3aa592ce27 |
| children | a2d4c30ba2f9 |
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| 9:21f1d1c5467b | 10:71af3ebbbb7a |
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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 <![CDATA[ | |
| 10 bedtools cluster | |
| 11 $strand | |
| 12 -d $distance | |
| 13 -i $inputA | |
| 14 > $output | |
| 15 ]]> | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | |
| 19 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness." | |
| 20 help="That is, only cluster features that are the same strand. By default, this is disabled." /> | |
| 21 <param name="distance" type="integer" value="0" | |
| 22 label="Maximum distance between features allowed for features to be clustered" | |
| 23 help="Default is 0. That is, overlapping and/or book-ended features are clustered." /> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data format_source="inputA" name="output" metadata_source="inputA"/> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="inputA" value="mergedBed1.bed" ftype="bed" /> | |
| 31 <output name="output" file="clusterBed_result.bed" ftype="bed" /> | |
| 32 </test> | |
| 33 </tests> | |
| 34 <help> | |
| 35 <![CDATA[ | |
| 36 **What it does** | |
| 37 | |
| 38 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. | |
| 39 | |
| 40 .. image:: $PATH_TO_IMAGES/cluster-glyph.png | |
| 41 | |
| 42 .. class:: warningmark | |
| 43 | |
| 44 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). | |
| 45 | |
| 46 @REFERENCES@ | |
| 47 ]]> | |
| 48 </help> | |
| 49 <expand macro="citations" /> | |
| 50 </tool> |