Mercurial > repos > iuc > rna_starsolo
changeset 15:b8f5f6e87f5c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit f6ccf9e6d01368c832110742b6f6534ff3b3b6a9
author | iuc |
---|---|
date | Thu, 09 Mar 2023 21:12:17 +0000 |
parents | 1cd2511a396e |
children | 13022c3d3076 |
files | macros.xml rg_rnaStarSolo.xml |
diffstat | 2 files changed, 70 insertions(+), 5 deletions(-) [+] |
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--- a/macros.xml Wed Feb 22 18:01:29 2023 +0000 +++ b/macros.xml Thu Mar 09 21:12:17 2023 +0000 @@ -5,7 +5,7 @@ the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ --> <!-- STAR version to be used --> <token name="@TOOL_VERSION@">2.7.10b</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">21.01</token> <!-- STAR index version compatible with this version of STAR This is the STAR version that introduced the index structure expected
--- a/rg_rnaStarSolo.xml Wed Feb 22 18:01:29 2023 +0000 +++ b/rg_rnaStarSolo.xml Thu Mar 09 21:12:17 2023 +0000 @@ -123,7 +123,7 @@ --soloOutFormatFeaturesGeneField3 '${solo.soloOutFormatFeaturesGeneField3}' ## Unmapped - '$solo.outSAMunmapped' + $solo.outSAMunmapped ## Read MAPQ --outSAMmapqUnique ${solo.outSAMmapqUnique} ## Limits @@ -132,11 +132,14 @@ ##outWig: @OUTWIG@ ## Rename the the selected features directory - && mv Solo.out/${solo.soloFeatures} Solo.out/soloFeatures + #if $solo.soloFeatures == 'Gene Velocyto' + && mv Solo.out/Velocyto Solo.out/soloFeatures + #else + && mv Solo.out/${solo.soloFeatures} Solo.out/soloFeatures + #end if ## put the barcodes and features stats into a single file && cat <(echo "Barcodes:") Solo.out/Barcodes.stats <(echo "Genes:") Solo.out/soloFeatures/Features.stats > '${output_stats}' - #if "CB" in $tag_names or "UB" in $tag_names or str($outWig.outWigType) != 'None': ## recompress BAM output for smaller file size && samtools view -b -o '$output_BAM' Aligned.sortedByCoord.out.bam @@ -157,7 +160,6 @@ #end if ##outWig: @OUTWIGOUTPUTS@ - ]]></command> <configfiles> <configfile name="manifest_file" > @@ -351,6 +353,7 @@ <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" > @@ -1241,6 +1244,68 @@ </assert_contents> </output> </test> + <test expect_num_outputs="6"> + <!-- test 12 --> + <conditional name="refGenomeSource"> + <param name="geneSource" value="history" /> + <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" /> + <param name="genomeSAindexNbases" value="4" /> + <param name="sjdbOverhang" value="100" /> + <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/> + </conditional> + <conditional name="sc" > + <param name="solo_type" value="CB_UMI_Simple" /> + <conditional name="input_types"> + <param name="use" value="repeat" /> + <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" /> + <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" /> + </conditional> + <param name="soloCBwhitelist" value="filtered.barcodes.txt" /> + <conditional name="params"> + <param name="chemistry" value="Cv3" /> + </conditional> + <conditional name="umidedup"> + <param name="soloUMIdedup" value="1MM_All" /> + </conditional> + </conditional> + <section name="solo" > + <conditional name="filter"> + <param name="filter_type" value="no_filter" /> + </conditional> + <param name="soloStrand" value="Forward" /> + <param name="soloFeatures" value="Gene Velocyto" /> + <param name="quantModeGene" value="true" /> + </section> + <output name="output_barcodes" > + <assert_contents> + <!-- first and last line --> + <has_line line="AAACCTGAGCGCTCCA" /> + <has_line line="TTTGGTTAGTGGGCTA" /> + <has_n_lines n="394" /> + </assert_contents> + </output> + <output name="output_genes"> + <assert_contents> + <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" /> + <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" /> + <has_n_lines n="14" /> + </assert_contents> + </output> + <output name="output_stats" > + <assert_contents> + <has_line_matching expression="\s+noUnmapped\s+0" /> + <has_line_matching expression="\s+yesUMIs\s+36" /> + </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> + <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" /> + </output> + </test> </tests> <help><![CDATA[ **What it does**