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comparison coverageBed.xml @ 11:7308cc546a36 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author iuc
date Mon, 17 Oct 2016 10:13:35 -0400
parents 2ab422b551df
children 18aeac3cd1db
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10:c78cf6fe3018 11:7308cc546a36
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@.0">
2 <description>of features in file B on the features in file A (bedtools coverage)</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" />
22 </command> 22 </command>
23 <inputs> 23 <inputs>
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" /> 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" />
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" /> 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" />
26 <expand macro="split" /> 26 <expand macro="split" />
27 <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"
28 help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to 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)"/>
29 <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue="" 29 <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue=""
30 label="Report the depth at each position in each A feature" 30 label="Report the depth at each position in each A feature"
31 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)" />
32 <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue="" 32 <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue=""
45 </tests> 45 </tests>
46 <help> 46 <help>
47 <![CDATA[ 47 <![CDATA[
48 **What it does** 48 **What it does**
49 49
50 `bedtools coverage`_ 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
51 file B on the features in file A. For example, ``bedtools coverage`` 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
52 (file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. 52 (file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest.
53 One advantage that ``bedtools coverage`` 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
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. 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.
55 Thus, ``bedtools coverage`` also computes the *breadth* of coverage for each interval in A. 55 Thus, ``bedtools coverage`` also computes the *breadth* of coverage for each interval in A.
56 56
57 .. _bedtools coverage: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html 57 .. _bedtools coverage: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html
58 58