Mercurial > repos > iuc > bedtools
diff coverageBed.xml @ 11:7308cc546a36 draft
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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--- a/coverageBed.xml Mon Oct 03 07:36:08 2016 -0400 +++ b/coverageBed.xml Mon Oct 17 10:13:35 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1"> +<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0"> <description>of features in file B on the features in file A (bedtools coverage)</description> <macros> <import>macros.xml</import> @@ -24,7 +24,7 @@ <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" /> <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" /> <expand macro="split" /> - <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" + <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/> <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Report the depth at each position in each A feature" @@ -47,10 +47,10 @@ <![CDATA[ **What it does** -`bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in -file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments -(file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. -One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that +`bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in +file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments +(file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. +One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that 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. Thus, ``bedtools coverage`` also computes the *breadth* of coverage for each interval in A.