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