comparison bedpeToBam.xml @ 17:44867b59dbf2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174

16:e0cec48a4695

<tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.0">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

    <command>
<![CDATA[
        bedtools bedpetobam
            -mapq $mapq
            -i '$input'
            -g $genome
            > '$output'
]]>
    </command>
    <inputs>
        <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file"/>
        <expand macro="genome" />
        <param name="mapq" type="integer" value="255"
            label="Set a mapping quality (SAM MAPQ field) value for all BED entries"
            help="(-mapq)" />
    </inputs>
    <outputs>
        <data format="bam" name="output" metadata_source="input"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
            <param name="genome" value="mm9.len"/>
            <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" />
        </test>
    </tests>
    <help>

17:44867b59dbf2

<tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.1">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

    <command>
<![CDATA[
        bedtools bedpetobam
            -mapq $mapq
            -i '$input'
            -g @GENOME_FILE@
            > '$output'
]]>
    </command>
    <inputs>
        <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file"/>
        <expand macro="input_conditional_genome_file" />
        <param name="mapq" type="integer" value="255"
            label="Set a mapping quality (SAM MAPQ field) value for all BED entries"
            help="(-mapq)" />
    </inputs>
    <outputs>
        <data format="bam" name="output" 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>