comparison artbio_bam_cleaning.xml @ 4:15ada8e1580a draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 13e2d0837000c2557f9590aa861a9fd5bc16cbcc"

3:a1462dd52f17

<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy3">
    <description>
        on flags and PCR Duplicates and MD recalibration
    </description>
    <macros>
        <import>macro.xml</import>

    @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
    && sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' -o $fullfilter $calmd
    ]]></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)" />
        <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)" />
    </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
============================

4:15ada8e1580a

<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy4">
    <description>
        on flags and PCR Duplicates and MD recalibration
    </description>
    <macros>
        <import>macro.xml</import>

    @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"
    #if $skip_rmdup == 'no':
        | samtools rmdup -s - - | tee $input_base".filt1.dedup.bam"
    #end if
    | bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
    | samtools calmd  -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa > $calmd
    && sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' -o $fullfilter $calmd
    ]]></command>
    <inputs>
        <expand macro="reference_source_conditional" />
        <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/>
            <param name="skip_rmdup" type="select" label="skip remove pcr duplicate step ?" display="radio"
                   help="useful if duplicates are already marked by other tools">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
    </inputs>
    <outputs>
        <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)" />
        <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)" />
    </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="calmd.bam" ftype="bam" />
            <output name="fullfilter" file="full.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="skip_rmdup" value="yes" />
            <param name="ref_file" value="chr21.fa" />
            <output name="calmd" file="normdup_calmd.bam" ftype="bam" />
            <output name="fullfilter" file="normdup_full.bam" ftype="bam" />
        </test>
    </tests>
    <help>
ARTbio bam cleaning overview
============================