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annotate clusterBed.xml @ 48:2f457890d8c8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
author iuc
date Tue, 11 Dec 2018 13:59:34 -0500
parents d279800f4ff9
children df28283b3778
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48
2f457890d8c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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1 <tool id="bedtools_clusterbed" name="bedtools ClusterBed" version="@WRAPPER_VERSION@">
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2 <description>cluster overlapping/nearby intervals</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 <![CDATA[
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10 bedtools cluster
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11 $strand
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12 -d $distance
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c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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13 -i '$inputA'
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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14 > '$output'
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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19 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness."
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20 help="That is, only cluster features that are the same strand. By default, this is disabled." />
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c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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21 <param name="distance" type="integer" value="0"
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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22 label="Maximum distance between features allowed for features to be clustered"
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23 help="Default is 0. That is, overlapping and/or book-ended features are clustered." />
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24 </inputs>
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25 <outputs>
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26 <data format_source="inputA" name="output" metadata_source="inputA"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="inputA" value="mergedBed1.bed" ftype="bed" />
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31 <output name="output" file="clusterBed_result.bed" ftype="bed" />
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32 </test>
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33 </tests>
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34 <help>
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35 <![CDATA[
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36 **What it does**
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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.
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40 .. image:: $PATH_TO_IMAGES/cluster-glyph.png
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41
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42 .. class:: warningmark
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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).
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45
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46 @REFERENCES@
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47 ]]>
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48 </help>
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49 <expand macro="citations" />
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50 </tool>