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comparison clusterBed.xml @ 50:df28283b3778 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:54:22 -0400
parents 2f457890d8c8
children 7a06bb42dbb1
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49:5074e81a5ce1 50:df28283b3778
1 <tool id="bedtools_clusterbed" name="bedtools ClusterBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_clusterbed" name="bedtools ClusterBed" version="@TOOL_VERSION@">
2 <description>cluster overlapping/nearby intervals</description> 2 <description>cluster overlapping/nearby intervals</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command><![CDATA[
9 <![CDATA[ 9 bedtools cluster
10 bedtools cluster 10 $strand
11 $strand 11 -d $distance
12 -d $distance 12 -i '$inputA'
13 -i '$inputA' 13 > '$output'
14 > '$output' 14 ]]></command>
15 ]]>
16 </command>
17 <inputs> 15 <inputs>
18 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 16 <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
19 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness." 17 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Force strandedness."
20 help="That is, only cluster features that are the same strand. By default, this is disabled." /> 18 help="That is, only cluster features that are the same strand. By default, this is disabled." />
21 <param name="distance" type="integer" value="0" 19 <param name="distance" argument="-d" type="integer" value="0"
22 label="Maximum distance between features allowed for features to be clustered" 20 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." /> 21 help="Default is 0. That is, overlapping and/or book-ended features are clustered." />
24 </inputs> 22 </inputs>
25 <outputs> 23 <outputs>
26 <data format_source="inputA" name="output" metadata_source="inputA"/> 24 <data name="output" format_source="inputA" metadata_source="inputA"/>
27 </outputs> 25 </outputs>
28 <tests> 26 <tests>
29 <test> 27 <test>
30 <param name="inputA" value="mergedBed1.bed" ftype="bed" /> 28 <param name="inputA" value="mergedBed1.bed" ftype="bed" />
31 <output name="output" file="clusterBed_result.bed" ftype="bed" /> 29 <output name="output" file="clusterBed_result.bed" ftype="bed" />
32 </test> 30 </test>
33 </tests> 31 </tests>
34 <help> 32 <help><![CDATA[
35 <![CDATA[
36 **What it does** 33 **What it does**
37 34
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. 35 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 36
40 .. image:: $PATH_TO_IMAGES/cluster-glyph.png 37 .. image:: $PATH_TO_IMAGES/cluster-glyph.png
42 .. class:: warningmark 39 .. class:: warningmark
43 40
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). 41 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 42
46 @REFERENCES@ 43 @REFERENCES@
47 ]]> 44 ]]></help>
48 </help>
49 <expand macro="citations" /> 45 <expand macro="citations" />
50 </tool> 46 </tool>