comparison bamToBed.xml @ 35:b28e0cfa7ba1 draft

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

34:dde39ba9c031

        <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
    </expand>
    <expand macro="stdio" />
    <command><![CDATA[
#if $input.extension == 'bam' and $option == "-bedpe":
    samtools sort -n '${input}' ./input &&
#else
    ln -s '${input}' ./input.bam &&
#end if

bedtools bamtobed

35:b28e0cfa7ba1

        <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
    </expand>
    <expand macro="stdio" />
    <command><![CDATA[
#if $input.extension == 'bam' and $option == "-bedpe":
    samtools sort -n -T "\${TMPDIR:-.}" '${input}' ./input &&
#else
    ln -s '${input}' ./input.bam &&
#end if

bedtools bamtobed