comparison ivar_trim.xml @ 3:5d6ed46cc101 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 47276c84cd0cd40084b7ccdf2e22c620ee1c10f6"

2:cb903c9dc33d

        -m $min_len
        -q $min_qual
        -s $window_width
        $inc_primers
        -p trimmed &&
        samtools sort -@ \${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam &&
        samtools index -@ \${GALAXY_SLOTS:-1} 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">

3:5d6ed46cc101

        -m $min_len
        -q $min_qual
        -s $window_width
        $inc_primers
        -p trimmed &&
        samtools sort -@ \${GALAXY_SLOTS:-1} -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">