comparison rgrnastar/rg_rnaStar.xml @ 12:f81bf1f1d924 draft

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11:94c94e25d61c

    --genomeDir ${refGenomeSource.index.fields.path} 
    --readFilesIn $input1 
    #if $singlePaired.sPaired == "paired"
            $singlePaired.input2
        #end if

        --runThreadN 4

    ## Parameters.
    --outSAMattributes "$outSAMattributes"
    #if $params.settingsType == "full":
        --chimSegmentMin $params.chim_segment_min
        --chimScoreMin $params.chim_score_min
    #end if

    ## may or may not need to generate SAM tags and handle non-canonicals for Cufflinks tools.
    ${outSAMstrandField} $outFilterIntronMotifs}

    ;

    ##
    ## BAM conversion.

            <when value="history">
                <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
            </when>
        </conditional>
            <param name="outSAMattributes" type="select" label="Include extra sam attributes for downstream processing">
              <option value="Standard">Standard - eg for old Samtools downstream</option>
              <option value="All" selected="true">All modern Samtools attributes - see below</option>
            </param>
            <param name="outSAMstrandField" type="select" label="Include extra sam attributes for downstream processing">
              <option value="--outSAMstrandField intronMotif" selected="true">Add XS for cufflinks</option>
              <option value="">No XS added to sam output</option>
            </param>

12:f81bf1f1d924

    --genomeDir ${refGenomeSource.index.fields.path} 
    --readFilesIn $input1 
    #if $singlePaired.sPaired == "paired"
            $singlePaired.input2
        #end if
        --runThreadN 4
    #if $params.settingsType == "full":
        --chimSegmentMin $params.chim_segment_min
        --chimScoreMin $params.chim_score_min
    #end if

    ## may or may not need to generate SAM tags and handle non-canonicals for Cufflinks tools.
    ${outSAMstrandField} ${outFilterIntronMotifs} ${outSAMattributes}

    ;

    ##
    ## BAM conversion.

            <when value="history">
                <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
            </when>
        </conditional>
            <param name="outSAMattributes" type="select" label="Include extra sam attributes for downstream processing">
              <option value="--outSAMattributes Standard">Standard - eg for old Samtools downstream</option>
              <option value="--outSAMattributes All" selected="true">All modern Samtools attributes - see below</option>
            </param>
            <param name="outSAMstrandField" type="select" label="Include extra sam attributes for downstream processing">
              <option value="--outSAMstrandField intronMotif" selected="true">Add XS for cufflinks</option>
              <option value="">No XS added to sam output</option>
            </param>