comparison bedpeToBam.xml @ 35:b28e0cfa7ba1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"

34:dde39ba9c031

<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
bedtools bedpetobam
-mapq $mapq
-i '$input'

        <expand macro="input_conditional_genome_file" />
        <param argument="-mapq" type="integer" value="255"
            label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
    </inputs>
    <outputs>
        <data name="output" format="bam" metadata_source="input"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="mm9.len"/>
            <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

35:b28e0cfa7ba1

<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <!-- bedtobam broken in 2.29.0 <expand macro="requirements" /> -->
    <requirements>
        <requirement type="package" version="2.27.1">bedtools</requirement>
    </requirements>
    <expand macro="stdio" />
    <command><![CDATA[
bedtools bedpetobam
-mapq $mapq
-i '$input'

        <expand macro="input_conditional_genome_file" />
        <param argument="-mapq" type="integer" value="255"
            label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
    </inputs>
    <outputs>
        <data name="output" format="unsorted.bam" metadata_source="input"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="mm9.len"/>
            <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="unsorted.bam" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**