comparison rg_rnaStar.xml @ 24:4df95e2d7f61 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17

23:a2b0feda6933

            <param argument="- -outSAMprimaryFlag" type="boolean"
            truevalue="AllBestScore" falsevalue="OneBestScore" checked="false"
            label="Would you like all alignments with the best score labeled
            primary?"/> -->
            <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" />
            <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value
            - according to SAM/BAM specs it means "undefined".
            - Using 255 as the max mapq causes problem with modern downstream tools like mutect2: https://sites.duke.edu/workblog/2021/08/18/star-rnaseq-gatk-mutect2/ and 60 has become an inofficial replacement for 255. -->
            <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255"
            label="MAPQ value for unique mappers"
            help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is
used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2." />
        </section>
        <section name="filter" title="Output filter criteria" expanded="true">
            <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true"
            label="Exclude the following records from the BAM output">
                <option value="exclude_unmapped">Unmapped reads</option>

                    <param argument="--outFilterMismatchNoverReadLmax" type="float" value="1" min="0" max="1" label="Maximum ratio of mismatches to read length" help="Alignments with a mismatch ratio of at least this value will not be output"/>
                    <param argument="--outFilterScoreMin" type="integer" value="0" min="0" label="Minimum alignment score" help="Alignments must have scores higher than this value to be output"/>
                    <param argument="--outFilterScoreMinOverLread" type="float" value="0.66" min="0" max="1" label="Minimum alignment score, normalized to read length" help="Alignments must have (normalized) scores higher than this value to be output"/>
                    <param argument="--outFilterMatchNmin" type="integer" value="0" min="0" label="Minimum number of matched bases" help="Alignments must have the number of matched bases higher than this value to be output"/>
                    <param argument="--outFilterMatchNminOverLread" type="float" value="0.66" min="0" max="1" label="Minimum number of matched bases, normalized to read length" help="Alignments must have the (normalized) number of matched bases higher than this value to be output"/>
                    <param argument="--outSAMmultNmax" type="integer" value="-1" min="-1" label="Maximum number of multimapping alignments to output for a read" help="A value of -1 (the default) results in all alignments (up to –-outFilterMultimapNmax) being output" />
                    <param argument="--outSAMtlen" type="select" label="Calculation method for TLEN">
                        <option value="1" selected="true">leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate</option>
                        <option value="2">leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends</option>
                    </param>
                </when>

            <expand macro="dbKeyActions" />
        </data>

        <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab">
            <filter>'GeneCounts' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter>
            <expand macro="dbKeyActions" />
            <expand macro="outCountActions" />
        </data>
        <expand macro="outWigOutputs"/>
    </outputs>

            </section>

            <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
            <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
            <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
            <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt" />
        </test>
        <!-- test gtf file and TranscriptomeSAM mode -->
        <test expect_num_outputs="4">
            <conditional name="singlePaired">
                <param name="sPaired" value="single" />

24:4df95e2d7f61

            <param argument="- -outSAMprimaryFlag" type="boolean"
            truevalue="AllBestScore" falsevalue="OneBestScore" checked="false"
            label="Would you like all alignments with the best score labeled
            primary?"/> -->
            <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" />
            <expand macro="outSAMmapqUnique"/>
        </section>
        <section name="filter" title="Output filter criteria" expanded="true">
            <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true"
            label="Exclude the following records from the BAM output">
                <option value="exclude_unmapped">Unmapped reads</option>

                    <param argument="--outFilterMismatchNoverReadLmax" type="float" value="1" min="0" max="1" label="Maximum ratio of mismatches to read length" help="Alignments with a mismatch ratio of at least this value will not be output"/>
                    <param argument="--outFilterScoreMin" type="integer" value="0" min="0" label="Minimum alignment score" help="Alignments must have scores higher than this value to be output"/>
                    <param argument="--outFilterScoreMinOverLread" type="float" value="0.66" min="0" max="1" label="Minimum alignment score, normalized to read length" help="Alignments must have (normalized) scores higher than this value to be output"/>
                    <param argument="--outFilterMatchNmin" type="integer" value="0" min="0" label="Minimum number of matched bases" help="Alignments must have the number of matched bases higher than this value to be output"/>
                    <param argument="--outFilterMatchNminOverLread" type="float" value="0.66" min="0" max="1" label="Minimum number of matched bases, normalized to read length" help="Alignments must have the (normalized) number of matched bases higher than this value to be output"/>
                    <param argument="--outSAMmultNmax" type="integer" value="-1" min="-1" label="Maximum number of multimapping alignments to output for a read" help="A value of -1 (the default) results in all alignments (up to --outFilterMultimapNmax) being output" />
                    <param argument="--outSAMtlen" type="select" label="Calculation method for TLEN">
                        <option value="1" selected="true">leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate</option>
                        <option value="2">leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends</option>
                    </param>
                </when>

            <expand macro="dbKeyActions" />
        </data>

        <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab">
            <filter>'GeneCounts' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter>
            <expand macro="outCountActions" />
        </data>
        <expand macro="outWigOutputs"/>
    </outputs>

            </section>

            <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
            <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
            <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
            <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt">
                <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
            </output>
        </test>
        <!-- test gtf file and TranscriptomeSAM mode -->
        <test expect_num_outputs="4">
            <conditional name="singlePaired">
                <param name="sPaired" value="single" />