comparison coverageBed.xml @ 11:7308cc546a36 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811

10:c78cf6fe3018

<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
    <description>of features in file B on the features in file A (bedtools coverage)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

    </command>
    <inputs>
        <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" 
            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"
            help="Positions reported are one based. Each position and depth follow the complete B feature (-d)" />
        <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue=""

    </tests>
    <help>
<![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 
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.

.. _bedtools coverage: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html

11:7308cc546a36

<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>
    </macros>
    <expand macro="requirements" />

    </command>
    <inputs>
        <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"
            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"
            help="Positions reported are one based. Each position and depth follow the complete B feature (-d)" />
        <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue=""

    </tests>
    <help>
<![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
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.

.. _bedtools coverage: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html