Mercurial > repos > iuc > rna_starsolo
diff rg_rnaStarSolo.xml @ 14:1cd2511a396e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
author | iuc |
---|---|
date | Wed, 22 Feb 2023 18:01:29 +0000 |
parents | 9ee34ba73ebf |
children | b8f5f6e87f5c |
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--- a/rg_rnaStarSolo.xml Fri Feb 17 20:04:43 2023 +0000 +++ b/rg_rnaStarSolo.xml Wed Feb 22 18:01:29 2023 +0000 @@ -122,6 +122,10 @@ --soloOutFormatFeaturesGeneField3 '${solo.soloOutFormatFeaturesGeneField3}' + ## Unmapped + '$solo.outSAMunmapped' + ## Read MAPQ + --outSAMmapqUnique ${solo.outSAMmapqUnique} ## Limits @LIMITS@ @@ -189,13 +193,13 @@ <param name="GTFselect" type="select" label="Reference genome with annotation" help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions, and provide your own splice junction annonations."> - <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option> + <option value="without-gtf-with-gtf" selected='true'>use genome reference without builtin gene-model</option> <option value="with-gtf">use genome reference with builtin gene-model</option> </param> <when value="with-gtf"> <expand macro="index_selection" with_gene_model="1" /> </when> - <when value="without-gtf"> + <when value="without-gtf-with-gtf"> <expand macro="index_selection" with_gene_model="0" /> <expand macro="SJDBOPTIONS"/> </when> @@ -325,7 +329,7 @@ <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs."> <expand macro="umidedup_options" /> <option value="Exact" >Exact</option> - <option value="NoDedup" >CellRanger2-4 algorithm</option> + <option value="NoDedup" >Do not deduplicate UMIs</option> </param> <when value="1MM_All"/> <when value="1MM_Directional_UMItools"/> @@ -388,12 +392,19 @@ <expand macro="common_SAM_attributes"/> <option value="CR">CR Cellular barcode sequence bases (uncorrected)</option> <option value="CY">CY Phred quality of the cellular barcode sequence in the CR tag</option> + <option value="UR">UR UMI (uncorrected)</option> + <option value="UY">UY Phred quality of the UMI</option> <option value="GX">GX Gene ID</option> <option value="GN">GN Gene name</option> <option value="CB">CB Cell identifier (corrected)</option> <option value="UB">UB UMI (corrected)</option> + <option value="sM">sM assessment of CB and UMI</option> + <option value="sS">sS sequence of the entire barcode (CB,UMI,adapter...)</option> + <option value="sQ">quality of the entire barcode</option> </param> <param name="quantModeGene" type="boolean" truevalue="GeneCounts" falsevalue="" checked="false" label="Output global gene count" help="Can be used by MultiQC" /> + <param argument="--outSAMunmapped" type="boolean" truevalue="--outSAMunmapped Within" falsevalue="--outSAMunmapped None" checked="false" label="Output unmapped reads in the BAM" /> + <expand macro="outSAMmapqUnique"/> <expand macro="limits" /> </section> <expand macro="outWig"/> @@ -457,7 +468,6 @@ <data format="txt" name="output_stats" label="${tool.name} on ${on_string}: Barcode/Feature Statistic Summaries"/> <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: combined reads per gene" from_work_dir="ReadsPerGene.out.tab"> <filter>solo['quantModeGene']</filter> - <expand macro="dbKeyActions" /> <expand macro="outCountActions" /> </data> <expand macro="outWigOutputs"/> @@ -537,11 +547,12 @@ <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> <test expect_num_outputs="6"> <!-- test 2 --> - <!-- same as above, but using custom and no reads_per_gene--> + <!-- same as above, but using custom, no reads_per_gene and include unmapped reads--> <conditional name="refGenomeSource"> <param name="geneSource" value="history" /> <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" /> @@ -568,6 +579,7 @@ <section name="solo" > <param name="soloStrand" value="Forward" /> <param name="soloFeatures" value="Gene" /> + <param name="outSAMunmapped" value="true" /> </section> <output name="output_barcodes_filtered" > <assert_contents> @@ -597,7 +609,11 @@ <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="output_BAM"> + <assert_contents> + <has_size value="884669" delta="80000" /> + </assert_contents> + </output> </test> <test expect_num_outputs="6"> <!-- test 3 --> @@ -1153,6 +1169,78 @@ </assert_contents> </output> </test> + <test expect_num_outputs="7"> + <!-- test 11 indexed --> + <conditional name="refGenomeSource"> + <param name="geneSource" value="indexed" /> + <conditional name="GTFconditional"> + <param name="GTFselect" value="without-gtf-with-gtf" /> + <param name="genomeDir" value="000" /> + <param name="sjdbOverhang" value="75"/> + <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/> + </conditional> + </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" /> + <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="GENE1\s+GENE1\s+Gene\s+Expression" /> + <has_n_lines n="1" /> + </assert_contents> + </output> + <output name="output_matrix" > + <assert_contents> + <has_line_matching expression="1\s+394\s+31" /> + <has_line_matching expression="1\s+2\s+1" /> + <has_n_lines n="34" /> + </assert_contents> + </output> + <output name="output_stats" > + <assert_contents> + <has_line_matching expression="\s+noUnmapped\s+6335" /> + <has_line_matching expression="\s+yesUMIs\s+33" /> + </assert_contents> + </output> + <output name="output_BAM"> + <assert_contents> + <has_size value="7133" delta="1000"/> + </assert_contents> + </output> + <output name="reads_per_gene" > + <assert_contents> + <has_line_matching expression="GENE1\s+41\s+41\s+0" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ **What it does**