Mercurial > repos > iuc > bedtools

comparison coverageBed.xml @ 6:d25966c8ddeb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6ce9a5a91d803b9ac9e743d9721ff0ccd2a5a59f-dirty
author iuc
date Sun, 22 May 2016 12:33:32 -0400
parents 82aac94b06c3
children 0232cdab3664
comparison
equal deleted inserted replaced
5:f8b7dc21b4ee 6:d25966c8ddeb
1 <tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1"> 1 <tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
2 <description>of features in file A across the features in file B (coverageBed)</description> 2 <description>of features in file B on the features in file A (bedtools coverage)</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>
9 <![CDATA[ 9 <![CDATA[
10 coverageBed 10 #set inputBs = "' '".join([str($file) for $file in $inputB])
11 #if $inputA.ext == "bam" 11
12 -abam '$inputA' 12 bedtools coverage
13 #else
14 -a '$inputA'
15 #end if
16 -b '$inputB'
17 $d 13 $d
18 $hist 14 $hist
19 $split 15 $split
20 $strandedness 16 $strandedness
17 -a '$inputA'
18 -b '$inputBs'
21 | sort -k1,1 -k2,2n 19 | sort -k1,1 -k2,2n
22 > '$output' 20 > '$output'
23 ]]> 21 ]]>
24 </command> 22 </command>
25 <inputs> 23 <inputs>
26 <param format="bed,bam,gff,gg3,vcf" name="inputA" type="data" label="Count how many intervals in this BED/VCF/GFF/BAM file (source)" /> 24 <param format="bam,bed,gff,gff3,vcf" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
27 <param format="bed,gff,gff3,vcf" name="inputB" type="data" label="overlap the intervals in this BED file (target)" /> 25 <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true" label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
28 <expand macro="split" /> 26 <expand macro="split" />
29 <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" 27 <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
30 help="That is, only features in A are only counted towards coverage in B if they are the same strand. (-s)"/> 28 help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/>
31 <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue="" 29 <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue=""
32 label="Report the depth at each position in each B feature" 30 label="Report the depth at each position in each A feature"
33 help="Positions reported are one based. Each position and depth follow the complete B feature. (-d)" /> 31 help="Positions reported are one based. Each position and depth follow the complete B feature (-d)" />
34 <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue="" 32 <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue=""
35 label="Report a histogram of coverage for each feature in B as well as a summary histogram for all features in B" 33 label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"
36 help="Additonal columns after each feature in B: 1) depth 2) # bases at depth 3) size of B 4) % of B at depth. (-hist)" /> 34 help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth (-hist)" />
37 </inputs> 35 </inputs>
38 <outputs> 36 <outputs>
39 <data format="bed" name="output" metadata_source="inputB" label="Count of overlaps in ${inputA.name} on ${inputB.name}"/> 37 <data format="bed" name="output" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
40 </outputs> 38 </outputs>
41 <tests> 39 <tests>
42 <test> 40 <test>
43 <param name="inputA" value="coverageBedA.bed" ftype="bed" /> 41 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
44 <param name="genome" value="coverageBedB.bed" ftype="bed" /> 42 <param name="genome" value="coverageBedB.bed" ftype="bed" />
47 </tests> 45 </tests>
48 <help> 46 <help>
49 <![CDATA[ 47 <![CDATA[
50 **What it does** 48 **What it does**
51 49
52 coverageBed_ computes both the depth and breadth of coverage of features in 50 `bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in
53 file A across the features in file B. For example, coverageBed can compute the coverage of sequence alignments 51 file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments
54 (file A) across 1 kilobase (arbitrary) windows (file B) tiling a genome of interest. 52 (file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest.
55 One advantage that coverageBed offers is that it not only counts the number of features that 53 One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that
56 overlap an interval in file B, it also computes the fraction of bases in B interval that were overlapped by one or more features. 54 overlap an interval in file A, it also computes the fraction of bases in the interval in A that were overlapped by one or more features.
57 Thus, coverageBed also computes the breadth of coverage for each interval in B. 55 Thus, ``bedtools coverage`` also computes the *breadth* of coverage for each interval in A.
58 56
59 .. _coverageBed: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html 57 .. _bedtools coverage: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html
60 58
61 .. class:: infomark 59 .. class:: infomark
62 60
63 The output file will be comprised of each interval from your original target BED file, plus an additional column indicating the number of intervals in your source file that overlapped that target interval. 61 The lines in the output will be comprised of each interval in A, followed by:
62
63 1. The number of features in B that overlapped (by at least one base pair) the A interval.
64 2. The number of bases in A that had non-zero coverage from features in B.
65 3. The length of the entry in A.
66 4. The fraction of bases in A that had non-zero coverage from features in B.
64 67
65 @REFERENCES@ 68 @REFERENCES@
66 ]]> 69 ]]>
67 </help> 70 </help>
68 <expand macro="citations" /> 71 <expand macro="citations" />