comparison rg_rnaStar.xml @ 27:79de45b5069b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32

26:3ea5a2a63fa2

            <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" />
                <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />

27:79de45b5069b

            <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 if an alternative feature can be provided as a splicing unit.
         If the splice feature set is not set correctly,
        "Fatal INPUT FILE error, no exon lines in the GTF file" is expected -->
        <test expect_num_outputs="4">
            <conditional name="singlePaired">
                <param name="sPaired" value="single" />
                <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
            </conditional>
            <conditional name="refGenomeSource">
                <param name="geneSource" value="history" />
                <param name="genomeFastaFiles" value="tophat_test.fa" />
                <param name="genomeSAindexNbases" value="5" />
                <conditional name="GTFconditional">
                    <param name="GTFselect" value="with-gtf" />
                    <param name="sjdbOverhang" value="75"/>
                    <param name="sjdbGTFfile" value="no_exon.gtf" ftype="gtf"/>
                    <param name="sjdbGTFfeatureExon" value="fakexon"/>
                    <conditional name="quantmode_output">
                        <param name="quantMode" value="GeneCounts"/>
                    </conditional>
                </conditional>
            </conditional>
            <section name="oformat">
                <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
            </section>
            <section name="algo">
                <conditional name="params">
                    <param name="settingsType" value="default" />
                </conditional>
            </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_fakexon.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" />
                <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />