comparison artbio_bam_cleaning.xml @ 11:6815060fb056 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 667afd5a5408321a31cdebab75b378e694deab07"

10:ba3e6a71acb8

<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy3">
    <description>
        on flags and PCR Duplicates and MD recalibration
    </description>
    <macros>
        <import>macro.xml</import>

    | samtools calmd  -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa
    #if $specify_outputs == 'just_calMD':
        > $calmd
    #else if $specify_outputs == 'both':
        | tee $calmd
        | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
    #else:
        | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
    #end if
    ]]></command>
    <inputs>
        <expand macro="reference_source_conditional" />
        <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/>

               display="radio"
               help="The tool first generates MD-recalibrated alignements, then discards
                     aberrant Mapping Quality alignements generated by calMD recalibration.
                     One, the other, or both types of outputs can be retained by the tool">
            <option value="just_calMD">Alignments are only MD-recalibrated (for split or discordant read aware variant callers)</option>
            <option value="calMDandMQ" selected="true">Alignments are MD-recalibrated AND mapping quality &gt; 254 are discarded (for snv and small indel callers)</option>
            <option value="both">Both types of outputs are retained</option>
        </param>
    </inputs>
    <outputs>
        <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)">

11:6815060fb056

<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy4">
    <description>
        on flags and PCR Duplicates and MD recalibration
    </description>
    <macros>
        <import>macro.xml</import>

    | samtools calmd  -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa
    #if $specify_outputs == 'just_calMD':
        > $calmd
    #else if $specify_outputs == 'both':
        | tee $calmd
        | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254 and proper_pair' -f 'bam' /dev/stdin > $fullfilter
    #else:
        | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254 and proper_pair' -f 'bam' /dev/stdin > $fullfilter
    #end if
    ]]></command>
    <inputs>
        <expand macro="reference_source_conditional" />
        <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/>

               display="radio"
               help="The tool first generates MD-recalibrated alignements, then discards
                     aberrant Mapping Quality alignements generated by calMD recalibration.
                     One, the other, or both types of outputs can be retained by the tool">
            <option value="just_calMD">Alignments are only MD-recalibrated (for split or discordant read aware variant callers)</option>
            <option value="calMDandMQ" selected="true">Alignments are MD-recalibrated AND mapping quality &gt; 254 are discarded AND only proper_pair flag is retained (for snv and small indel callers)</option>
            <option value="both">Both types of outputs are retained</option>
        </param>
    </inputs>
    <outputs>
        <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)">