comparison artbio_bam_cleaning.xml @ 1:b550841f568b draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 2d441fd84bf17c0899d0b57ea35c84cb83b77119"

0:65d6d2b554b3

<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy0">
    <description>
        on flags and PCR Duplicates and MD recalibration
    </description>
    <macros>
        <import>macro.xml</import>

    @pipefail@
    @set_fasta_index@
    #set input_base = 'input'   
    ln -f -s $input_bam.metadata.bam_index input.bam.bai &&
    ln -s $input_bam input.bam &&
    sambamba view -h -t 8 --filter='mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped)' -f 'bam' $input_base".bam"
    | samtools rmdup - -
    |tee $input_base".filt1.dedup.bam"| bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
    | samtools calmd  -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa > $input_base".filt1.dedup.bamleft.calmd.bam" &&
    sambamba view -h -t 8 --filter='mapping_quality <= 254' -f 'bam' -o $input_base".filt1.dedup.bamleft.calmd.filt2.bam" $input_base".filt1.dedup.bamleft.calmd.bam"
    ]]></command>
    <inputs>
        <expand macro="reference_source_conditional" />
        <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/>
    </inputs>
    <outputs>
        <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)" from_work_dir="./input.filt1.dedup.bamleft.calmd.bam"/>
        <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)" from_work_dir="./input.filt1.dedup.bamleft.calmd.filt2.bam"/>
    </outputs>
    <tests>
        <test>
            <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" />
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" value="chr21.fa" />
            <output name="calmd" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.bam" ftype="bam" />
            <output name="fullfilter" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.filt2.bam" ftype="bam" />
        </test>
    </tests>
    <help>
ARTbio bam cleaning overview
============================

1:b550841f568b

<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy1">
    <description>
        on flags and PCR Duplicates and MD recalibration
    </description>
    <macros>
        <import>macro.xml</import>

    @pipefail@
    @set_fasta_index@
    #set input_base = 'input'   
    ln -f -s $input_bam.metadata.bam_index input.bam.bai &&
    ln -s $input_bam input.bam &&
    sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped)' -f 'bam' $input_base".bam"
    | samtools rmdup - -
    |tee $input_base".filt1.dedup.bam"| bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
    | samtools calmd  -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa > $calmd
    #if $pipeline == 'fullfilter':
    && sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' -o $fullfilter $calmd
    #end if
    ]]></command>
    <inputs>
        <expand macro="reference_source_conditional" />
        <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/>
        <param name="pipeline" type="select" label="where to stop the pipeline">
            <option value="CalMD">At CalMD processing, to keep split read alignments</option>
            <option value="fullfilter" selected="true">Full bam processing, will eliminate split read alignments in the final bam file</option>
        </param>
    </inputs>
    <outputs>
        <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)">
            <filter>pipeline == 'CalMD'</filter>
        </data>
        <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)">
             <filter>pipeline == 'fullfilter'</filter>
        </data>
       
    </outputs>
    <tests>
        <test>
            <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" />
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" value="chr21.fa" />
            <output name="fullfilter" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.filt2.bam" ftype="bam" />
        </test>
        <test>
            <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" />
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" value="chr21.fa" />
            <param name="pipeline" value="CalMD"/>
            <output name="calmd" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.bam" ftype="bam" />
        </test>
    </tests>
    <help>
ARTbio bam cleaning overview
============================