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annotate clusterBed.xml @ 39:3e38c9b3214f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
author iuc
date Wed, 01 Sep 2021 11:04:15 +0000
parents dde39ba9c031
children 7ab85ac5f64b
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3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
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1 <tool id="bedtools_clusterbed" name="bedtools ClusterBed" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>cluster overlapping/nearby intervals</description>
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3 <expand macro="bio_tools" />
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <command><![CDATA[
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10 bedtools cluster
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11 $strand
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12 -d $distance
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13 -i '$inputA'
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14 > '$output'
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15 ]]></command>
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16 <inputs>
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17 <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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18 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Force strandedness."
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19 help="That is, only cluster features that are the same strand. By default, this is disabled." />
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20 <param name="distance" argument="-d" type="integer" value="0"
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21 label="Maximum distance between features allowed for features to be clustered"
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22 help="Default is 0. That is, overlapping and/or book-ended features are clustered." />
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23 </inputs>
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24 <outputs>
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25 <data name="output" format_source="inputA" metadata_source="inputA"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="inputA" value="mergedBed1.bed" ftype="bed" />
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30 <output name="output" file="clusterBed_result.bed" ftype="bed" />
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34 **What it does**
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36 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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38 .. image:: $PATH_TO_IMAGES/cluster-glyph.png
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40 .. class:: warningmark
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42 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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43
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44 @REFERENCES@
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45 ]]></help>
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46 <expand macro="citations" />
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47 </tool>