comparison ivar_trim.xml @ 16:28e4bcbc86e7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 51d656555f9635bb8988f9eec904ee66657736e1

15:a2b94388d00d

        #else:
            -m $trimmed_length.min_len
        #end if
        -q $min_qual
        -s $window_width
        ## since v1.4 ivar trim *almost* supports piping its output, but
        ## unfortunately still writes *some* regular messages to stdout,
        ## so we need to stick writing to an intermediate file for now and
        ## want to unify the output stream
        -p trimmed 1>&2 &&
        samtools sort -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o trimmed.sorted.bam trimmed.bam
    ]]></command>
    <inputs>
        <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
        <conditional name="primer">
            <param label="Source of primer information" name="source" type="select">

16:28e4bcbc86e7

        #else:
            -m $trimmed_length.min_len
        #end if
        -q $min_qual
        -s $window_width
        | samtools sort -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o trimmed.sorted.bam -
    ]]></command>
    <inputs>
        <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
        <conditional name="primer">
            <param label="Source of primer information" name="source" type="select">