comparison mapBed.xml @ 26:95a3b2c25bd1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59

25:e36671a0f646

        @GENOME_FILE_MAPBED@
        > "${output}"
]]>
    </command>
    <inputs>
        <param format="bam,bed,vcf,gff,gff3" name="inputA" type="data" label="File A (BAM/BED/VCF/GFF)" />
        <param format="bam,bed,gff,vcf,gff3" name="inputB" type="data" label="File B (BAM/BED/VCF/GFF)" />
        <expand macro="overlap" />
        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
            label="Require reciprocal overlap"
            help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" />
        <expand macro="strand2" />

26:95a3b2c25bd1

        @GENOME_FILE_MAPBED@
        > "${output}"
]]>
    </command>
    <inputs>
        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
        <expand macro="overlap" />
        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
            label="Require reciprocal overlap"
            help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" />
        <expand macro="strand2" />