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comparison mergeBed.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
comparison
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49:5074e81a5ce1 50:df28283b3778
1 <tool id="bedtools_mergebed" name="bedtools MergeBED" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@">
2 <description>combine overlapping/nearby intervals into a single interval</description> 2 <description>combine overlapping/nearby intervals into a single interval</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 mergeBed
10 mergeBed 10 -i '${input}'
11 -i "${input}" 11 $strand
12 $strand 12 -d $distance
13 -d $distance 13 $header
14 $header 14 @C_AND_O_ARGUMENT@
15 @C_AND_O_ARGUMENT@ 15 > '${output}'
16 > "${output}" 16 ]]></command>
17 ]]>
18 </command>
19 <inputs> 17 <inputs>
20 <param name="input" format="bam,@STD_BEDTOOLS_INPUTS@" type="data" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/> 18 <param name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/>
21 <param name="strand" type="select" label="Calculation based on strandedness?"> 19 <param name="strand" type="select" label="Calculation based on strandedness?">
22 <option value="" selected="True">Overlaps on either strand</option> 20 <option value="" selected="true">Overlaps on either strand</option>
23 <option value="-s">Force strandedness. That is, only merge features that are the same strand.</option> 21 <option value="-s">Force strandedness. That is, only merge features that are the same strand (-s)</option>
24 <option value="-S +">Force merge for forward strand only.</option> 22 <option value="-S +">Force merge for forward strand only (-S +)</option>
25 <option value="-S -">Force merge for reverse strand only.</option> 23 <option value="-S -">Force merge for reverse strand only (-S -)</option>
26 </param> 24 </param>
27 <param name="distance" type="integer" value="0" 25 <param name="distance" argument="-d" type="integer" value="0"
28 label="Maximum distance between features allowed for features to be merged" 26 label="Maximum distance between features allowed for features to be merged"
29 help="That is, overlapping and/or book-ended features are merged. (-d)"/> 27 help="That is, overlapping and/or book-ended features are merged"/>
30 <expand macro="print_header" /> 28 <expand macro="print_header" />
31 <expand macro="c_and_o_argument"> 29 <expand macro="c_and_o_argument">
32 <param name="col" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" help="(-c)" /> 30 <param name="col" argument="-c" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" />
33 </expand> 31 </expand>
34 </inputs> 32 </inputs>
35 <outputs> 33 <outputs>
36 <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/> 34 <data name="output" format="bed" metadata_source="input" label="Merged ${input.name}"/>
37 </outputs> 35 </outputs>
38 <tests> 36 <tests>
39 <test> 37 <test>
40 <param name="input" value="mergedBed1.bed" ftype="bed" /> 38 <param name="input" value="mergedBed1.bed" ftype="bed" />
41 <output name="output" file="mergedBed_result1.bed" ftype="bed" /> 39 <output name="output" file="mergedBed_result1.bed" ftype="bed" />
63 <param name="operation" value="count"/> 61 <param name="operation" value="count"/>
64 </repeat> 62 </repeat>
65 <output name="output" file="mergedBed_result5.bed" ftype="bed" /> 63 <output name="output" file="mergedBed_result5.bed" ftype="bed" />
66 </test> 64 </test>
67 </tests> 65 </tests>
68 <help> 66 <help><![CDATA[
69 <![CDATA[
70 **What it does** 67 **What it does**
71 68
72 bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features. 69 bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features.
73 70
74 71
141 $ bedtools merge -i A.bed -d 1000 138 $ bedtools merge -i A.bed -d 1000
142 chr1 100 200 1000 139 chr1 100 200 1000
143 140
144 141
145 @REFERENCES@ 142 @REFERENCES@
146 ]]> 143 ]]></help>
147 </help>
148 <expand macro="citations" /> 144 <expand macro="citations" />
149 </tool> 145 </tool>