comparison rg_rnaStarSolo.xml @ 20:45795f582ae9 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151

19:42ce70172b72

            #if $sc.input_types_smart_seq.paired_end_collection[0].forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
                @FASTQ_GZ_OPTION@
            #end if
        #end if
    --soloCBwhitelist None
    #end if

    --soloStrand $solo.soloStrand
    --soloFeatures $solo.soloFeatures
    --soloUMIdedup $sc.umidedup.soloUMIdedup

                <option value="GeneFull" >Full: Count all reads overlapping genes' exons and introns</option>
                <option value="GeneFull_ExonOverIntron" >Full: Count all reads overlapping genes' exons and introns: prioritize 100% overlap with exons</option>
                <option value="GeneFull_Ex50pAS" >Full: Count all reads overlapping genes' exons and introns: prioritize 50% overlap with exons. Do not count reads with 100% exonic overlap in the antisense direction.</option>
                <option value="Gene Velocyto">Velocyto: calculate spliced, unspliced, and ambiguous counts per cell per gene similar to the velocyto tool</option>
            </param>
            <conditional name="filter" >
                <param name="filter_type" type="select" label="Cell filtering type and parameters" >
                    <option value="cellranger2" selected="true" >Simple filtering of CellRanger v2</option>
                    <option value="emptydrops" >EmptyDrops filtering in CellRanger flavor</option>
                    <option value="topcells" >Filter top N cells</option>

                    <param name="filter_type" value="no_filter" />
                </conditional>
                <param name="soloStrand" value="Forward" />
                <param name="soloFeatures" value="Gene" />
                <param name="quantModeGene" value="true" />
            </section>
            <output name="output_barcodes" >
                <assert_contents>
                    <!-- first and last line -->
                    <has_line line="AAACCTGAGCGCTCCA" />

                <assert_contents>
                    <has_line_matching expression="\s+noUnmapped\s+5823" />
                    <has_line_matching expression="\s+yesUMIs\s+8" />
                </assert_contents>
            </output>
            <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" />
            <output name="reads_per_gene" >
                <assert_contents>
                    <has_line_matching expression="ENSG00000279493\s+0\s+0\s+0" />
                    <has_line_matching expression="ENSG00000275464\s+38\s+1\s+40" />
                </assert_contents>

20:45795f582ae9

            #if $sc.input_types_smart_seq.paired_end_collection[0].forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
                @FASTQ_GZ_OPTION@
            #end if
        #end if
    --soloCBwhitelist None
    #end if

    #if $solo.wasp_conditional.waspOutputMode == "wasp_mode":
        --waspOutputMode SAMtag
        --varVCFfile '$solo.wasp_conditional.varVCFfile'
    #end if

    --soloStrand $solo.soloStrand
    --soloFeatures $solo.soloFeatures
    --soloUMIdedup $sc.umidedup.soloUMIdedup

                <option value="GeneFull" >Full: Count all reads overlapping genes' exons and introns</option>
                <option value="GeneFull_ExonOverIntron" >Full: Count all reads overlapping genes' exons and introns: prioritize 100% overlap with exons</option>
                <option value="GeneFull_Ex50pAS" >Full: Count all reads overlapping genes' exons and introns: prioritize 50% overlap with exons. Do not count reads with 100% exonic overlap in the antisense direction.</option>
                <option value="Gene Velocyto">Velocyto: calculate spliced, unspliced, and ambiguous counts per cell per gene similar to the velocyto tool</option>
            </param>
            <expand macro="wasp"/>
            <conditional name="filter" >
                <param name="filter_type" type="select" label="Cell filtering type and parameters" >
                    <option value="cellranger2" selected="true" >Simple filtering of CellRanger v2</option>
                    <option value="emptydrops" >EmptyDrops filtering in CellRanger flavor</option>
                    <option value="topcells" >Filter top N cells</option>

                    <param name="filter_type" value="no_filter" />
                </conditional>
                <param name="soloStrand" value="Forward" />
                <param name="soloFeatures" value="Gene" />
                <param name="quantModeGene" value="true" />
                <conditional name="wasp_conditional">
                    <param name="waspOutputMode" value="wasp_mode"/>
                    <param name="varVCFfile" value="filtered3.vcf" ftype="vcf" />
                </conditional>
            </section>
            <output name="output_barcodes" >
                <assert_contents>
                    <!-- first and last line -->
                    <has_line line="AAACCTGAGCGCTCCA" />

                <assert_contents>
                    <has_line_matching expression="\s+noUnmapped\s+5823" />
                    <has_line_matching expression="\s+yesUMIs\s+8" />
                </assert_contents>
            </output>
            <output name="output_BAM" value="filtered4.bam" ftype="bam" lines_diff="6"/>
            <output name="reads_per_gene" >
                <assert_contents>
                    <has_line_matching expression="ENSG00000279493\s+0\s+0\s+0" />
                    <has_line_matching expression="ENSG00000275464\s+38\s+1\s+40" />
                </assert_contents>