Mercurial > repos > iuc > bedtools

comparison mergeBed.xml @ 1:82aac94b06c3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
parents b8348686a0b9
children 457b09031d57
comparison
equal deleted inserted replaced
0:b8348686a0b9 1:82aac94b06c3
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>
9 mergeBed 9 <![CDATA[
10 -i $input 10 mergeBed
11 $strandedness 11 -i "${input}"
12 $report_number 12 $strand
13 -d $distance 13 -d $distance
14 $nms 14 $header
15 #if str($scores) != 'none' 15 > "${output}"
16 -scores $scores 16 ]]>
17 #end if
18 &gt; $output
19 </command> 17 </command>
20 <inputs> 18 <inputs>
21 <param name="input" format="bed,gff,vcf" type="data" label="Sort the following BED/VCF/GFF file"/> 19 <param name="input" format="bam,bed,gff,vcf" type="data" label="Sort the following BAM/BED/VCF/GFF file"/>
22 <param name="strandedness" type="boolean" label="Force strandedness." truevalue="-s" falsevalue="" checked="false" 20 <param name="strand" type="select" label="Calculation based on strandedness?">
23 help="That is, only merge features that are the same strand."/> 21 <option value="" selected="True">Overlaps on either strand</option>
24 <param name="report_number" type="boolean" label="Report the number of BED entries that were merged." truevalue="-n" falsevalue="" checked="false" 22 <option value="-s">Force strandedness. That is, only merge features that are the same strand.</option>
25 help="1 is reported if no merging occurred."/> 23 <option value="-S +">Force merge for forward strand only.</option>
26 <param name="nms" type="boolean" label="Report the names of the merged features separated by commas." truevalue="-nms" falsevalue="" checked="false" 24 <option value="-S -">Force merge for reverse strand only.</option>
27 help="1 is reported if no merging occurred."/> 25 </param>
28 26 <param name="distance" type="integer" value="0"
29 <param name="distance" type="integer" value="0" label="Maximum distance between features allowed for features to be merged." 27 label="Maximum distance between features allowed for features to be merged"
30 help="That is, overlapping and/or book-ended features are merged."/> 28 help="That is, overlapping and/or book-ended features are merged. (-d)"/>
31 <param name="scores" type="select" label="Report the scores of the merged features as"> 29 <expand macro="print_header" />
32 <option value="none" selected="True">Do not report at all</option> 30 <expand macro="choose_columns" />
33 <option value="sum">Sum</option> 31 <expand macro="choose_operations">
34 <expand macro="math_options" /> 32 <expand macro="math_options" />
35 </param> 33 <expand macro="additional_math_options" />
34 </expand>
36 </inputs> 35 </inputs>
37 <outputs> 36 <outputs>
38 <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/> 37 <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
39 </outputs> 38 </outputs>
40 <tests> 39 <tests>
41 <test> 40 <test>
42 <param name="input" value="0.bed" ftype="bed" /> 41 <param name="input" value="mergedBed1.bed" ftype="bed" />
43 <output name="output" file="0_result.bed" ftype="bed" /> 42 <output name="output" file="mergedBed_result1.bed" ftype="bed" />
44 </test> 43 </test>
45 <test> 44 <test>
46 <param name="input" value="1.bed" ftype="bed" /> 45 <param name="input" value="mergedBed2.bed" ftype="bed" />
47 <param name="strandedness" value="-s" /> 46 <param name="strandedness" value="-s" />
48 <output name="output" file="1_result.bed" ftype="bed" /> 47 <output name="output" file="mergedBed_result2.bed" ftype="bed" />
49 </test> 48 </test>
50 <test> 49 <test>
51 <param name="input" value="2.bed" ftype="bed" /> 50 <param name="input" value="mergedBed3.bed" ftype="bed" />
52 <param name="report_number" value="-n" /> 51 <param name="report_number" value="-n" />
53 <output name="output" file="2_result.bed" ftype="bed" /> 52 <output name="output" file="mergedBed_result3.bed" ftype="bed" />
54 </test> 53 </test>
55 <test> 54 <test>
56 <param name="input" value="3.bed" ftype="bed" /> 55 <param name="input" value="mergedBed4.bed" ftype="bed" />
57 <param name="distance" value="1000" /> 56 <param name="distance" value="1000" />
58 <output name="output" file="3_result.bed" ftype="bed" /> 57 <output name="output" file="mergedBed_result4.bed" ftype="bed" />
59 </test> 58 </test>
60 </tests> 59 </tests>
61 <help> 60 <help>
62 61 <![CDATA[
63 **What it does** 62 **What it does**
64 63
65 bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features. 64 bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features.
66 65
67 66
195 chr1 100 500 3 194 chr1 100 500 3
196 195
197 $ bedtools merge -i A.bed -scores collapse 196 $ bedtools merge -i A.bed -scores collapse
198 chr1 100 500 1,2,3 197 chr1 100 500 1,2,3
199 198
200
201 @REFERENCES@ 199 @REFERENCES@
200 ]]>
202 </help> 201 </help>
203 <expand macro="citations" /> 202 <expand macro="citations" />
204 </tool> 203 </tool>