| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy4 |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy3 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.7a |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.6a |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.5b |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.2b1 |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.2b |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.2a1 |
| toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.2a |
| rna_starsolo |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| star | 2.7.10b | package |
| samtools | 1.16.1 | package |
| gzip | 1.12 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz refGenomeSource|genomeSAindexNbases: 4 refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf refGenomeSource|sjdbOverhang: 100 refGenomeSource|geneSource: history sc|input_types|input1: pbmc_1k_v2_L001.R1.10k.fastq.gz sc|input_types|input2: pbmc_1k_v2_L001.R2.10k.fastq.gz sc|input_types|use: repeat sc|soloCBwhitelist: filtered.barcodes.txt sc|params|chemistry: Cv3 sc|umidedup|soloUMIdedup: 1MM_All sc|solo_type: CB_UMI_Simple solo|soloStrand: Forward solo|soloFeatures: Gene solo|filter|filter_type: no_filter solo|quantModeGene: True |
name: value name: value name: value name: value name: value name: value |
filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf pbmc_1k_v2_L001.R1.10k.fastq.gz pbmc_1k_v2_L001.R2.10k.fastq.gz filtered.barcodes.txt value |
| Test-2 |
refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz refGenomeSource|genomeSAindexNbases: 4 refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf refGenomeSource|sjdbOverhang: 100 refGenomeSource|geneSource: history sc|input_types|input1: pbmc_1k_v2_L001.R1.10k.fastq.gz sc|input_types|input2: pbmc_1k_v2_L001.R2.10k.fastq.gz sc|input_types|use: repeat sc|soloCBwhitelist: filtered.barcodes.txt sc|params|soloCBstart: 1 sc|params|soloCBlen: 16 sc|params|soloUMIstart: 17 sc|params|soloUMIlen: 12 sc|params|chemistry: custom sc|solo_type: CB_UMI_Simple solo|soloStrand: Forward solo|soloFeatures: Gene solo|outSAMunmapped: True |
name: value name: value name: value name: value name: value |
filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf pbmc_1k_v2_L001.R1.10k.fastq.gz pbmc_1k_v2_L001.R2.10k.fastq.gz filtered.barcodes.txt value |
| Test-3 |
refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz refGenomeSource|genomeSAindexNbases: 4 refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf refGenomeSource|sjdbOverhang: 100 refGenomeSource|geneSource: history sc|input_types|input1: ['pbmc_1k_v2_L001.R1.10k.fastq.gz', 'pbmc_1k_v2_L001.R1.10k.fastq.gz', 'pbmc_1k_v2_L001.R1.10k.fastq.gz'] sc|input_types|input2: ['pbmc_1k_v2_L001.R2.10k.fastq.gz', 'pbmc_1k_v2_L001.R2.10k.fastq.gz', 'pbmc_1k_v2_L001.R2.10k.fastq.gz'] sc|input_types|use: repeat sc|soloCBwhitelist: filtered.barcodes.txt sc|params|chemistry: Cv3 sc|umidedup|soloUMIdedup: 1MM_All sc|solo_type: CB_UMI_Simple solo|soloStrand: Forward solo|soloFeatures: Gene |
name: value name: value |
filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf pbmc_1k_v2_L001.R1.10k.fastq.gz pbmc_1k_v2_L001.R2.10k.fastq.gz filtered.barcodes.txt value |
| Test-4 |
refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz refGenomeSource|genomeSAindexNbases: 4 refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf refGenomeSource|sjdbOverhang: 100 refGenomeSource|geneSource: history sc|input_types|input_collection: paired collection sc|input_types|use: list_paired sc|soloCBwhitelist: filtered.barcodes.txt sc|params|chemistry: Cv3 sc|umidedup|soloUMIdedup: 1MM_All sc|solo_type: CB_UMI_Simple solo|soloStrand: Forward solo|soloFeatures: Gene outWig|outWigType: bedGraph |
name: value name: value name: value name: value name: value name: value |
filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf pbmc_1k_v2_L001.R1.10k.fastq.gz pbmc_1k_v2_L001.R2.10k.fastq.gz filtered.barcodes.txt value |
| Test-5 |
refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz refGenomeSource|genomeSAindexNbases: 4 refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf refGenomeSource|sjdbOverhang: 100 refGenomeSource|geneSource: history sc|input_types|input1: pbmc_1k_v2_L001.R1.10k.fastq.gz sc|input_types|input2: pbmc_1k_v2_L001.R2.10k.fastq.gz sc|input_types|use: repeat sc|soloCBwhitelist: filtered.barcodes.txt sc|params|chemistry: Cv3 sc|umidedup|soloUMIdedup: 1MM_All sc|soloCBmatchWLtype: 1MM_multi_pseudocounts sc|solo_type: CB_UMI_Simple solo|soloStrand: Forward solo|soloFeatures: GeneFull solo|filter|n_cells: 5 solo|filter|output_raw: True solo|filter|filter_type: topcells solo|soloOutFormatFeaturesGeneField3: Dummy Text |
name: value name: value name: value name: value name: value name: value |
filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf pbmc_1k_v2_L001.R1.10k.fastq.gz pbmc_1k_v2_L001.R2.10k.fastq.gz filtered.barcodes.txt value |
| Test-6 |
refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz refGenomeSource|genomeSAindexNbases: 4 refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf refGenomeSource|sjdbOverhang: 100 refGenomeSource|geneSource: history sc|input_types|input1: pbmc_1k_v2_L001.R1.10k.fastq.gz sc|input_types|input2: pbmc_1k_v2_L001.R2.10k.fastq.gz sc|input_types|use: repeat sc|soloCBwhitelist: filtered.barcodes.txt sc|params|chemistry: Cv3 sc|umidedup|soloUMIdedup: 1MM_All sc|solo_type: CB_UMI_Simple solo|soloStrand: Forward solo|soloFeatures: Gene solo|filter|nExpectedCells: 5 solo|filter|maxPercentile: 0.99 solo|filter|maxMinRatio: 10 solo|filter|indMin: 45000 solo|filter|indMax: 90000 solo|filter|umiMin: 500 solo|filter|umiMinFracMedian: 0.01 solo|filter|candMaxN: 20000 solo|filter|FDR: 0.01 solo|filter|simN: 10000 solo|filter|filter_type: emptydrops |
name: value name: value name: value name: value name: value |
filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf pbmc_1k_v2_L001.R1.10k.fastq.gz pbmc_1k_v2_L001.R2.10k.fastq.gz filtered.barcodes.txt value |
| Test-7 |
refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz refGenomeSource|genomeSAindexNbases: 4 refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf refGenomeSource|sjdbOverhang: 100 refGenomeSource|geneSource: history sc|input_types|input1: indrop.R1.fastq.gz sc|input_types|input2: indrop.R2.fastq.gz sc|input_types|use: repeat sc|cb_whitelists_0|whitelist_file: indrop.barcodes1.txt sc|cb_whitelists_0|cb_start_anchor: 0 sc|cb_whitelists_0|cb_start_anchor_pos: 0 sc|cb_whitelists_0|cb_end_anchor: 2 sc|cb_whitelists_0|cb_end_anchor_pos: -1 sc|cb_whitelists_1|whitelist_file: indrop.barcodes2.txt sc|cb_whitelists_1|cb_start_anchor: 3 sc|cb_whitelists_1|cb_start_anchor_pos: 1 sc|cb_whitelists_1|cb_end_anchor: 3 sc|cb_whitelists_1|cb_end_anchor_pos: 8 sc|umi_start_anchor: 3 sc|umi_start_anchor_pos: 9 sc|umi_end_anchor: 3 sc|umi_end_anchor_pos: 14 sc|soloAdapterSequence: GAGTGATTGCTTGTGACGCCTT sc|soloAdapterMismatchesNmax: 1 sc|clipAdapterType: CellRanger4 sc|umidedup|soloUMIdedup: 1MM_All sc|soloCBmatchWLtype: 1MM sc|solo_type: CB_UMI_Complex |
name: value name: value name: value name: value |
filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf indrop.R1.fastq.gz indrop.R2.fastq.gz indrop.barcodes1.txt indrop.barcodes2.txt value |
| Test-8 |
refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz refGenomeSource|genomeSAindexNbases: 4 refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf refGenomeSource|sjdbOverhang: 100 refGenomeSource|geneSource: history sc|input_types_smart_seq|paired_end_collection: list:paired collection sc|input_types_smart_seq|use: list_paired_end sc|cell_ids: smartseq.cellids.txt sc|umidedup|soloUMIdedup: Exact sc|solo_type: SmartSeq solo|soloStrand: Unstranded solo|filter|n_cells: 2 solo|filter|filter_type: topcells |
name: value name: value name: value name: value |
filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf smartseq1.R1.fastq.gz smartseq1.R2.fastq.gz smartseq2.R1.fastq.gz smartseq2.R2.fastq.gz smartseq3.R1.fastq.gz smartseq3.R2.fastq.gz smartseq4.R1.fastq.gz smartseq4.R2.fastq.gz smartseq5.R1.fastq.gz smartseq5.R2.fastq.gz smartseq6.R1.fastq.gz smartseq6.R2.fastq.gz smartseq7.R1.fastq.gz smartseq7.R2.fastq.gz smartseq8.R1.fastq.gz smartseq8.R2.fastq.gz smartseq9.R1.fastq.gz smartseq9.R2.fastq.gz smartseq.cellids.txt value |
| Test-9 |
refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz refGenomeSource|genomeSAindexNbases: 4 refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf refGenomeSource|sjdbOverhang: 100 refGenomeSource|geneSource: history sc|input_types|input1: pbmc_1k_v2_L001.R1.10k.fastq.gz sc|input_types|input2: pbmc_1k_v2_L001.R2.10k.fastq.gz sc|input_types|use: repeat sc|soloCBwhitelist: filtered.barcodes.txt sc|params|chemistry: Cv3 sc|umidedup|soloUMIdedup: 1MM_All sc|solo_type: CB_UMI_Simple solo|soloStrand: Forward solo|soloFeatures: Gene solo|filter|filter_type: no_filter solo|outSAMattributes: ['NH', 'HI', 'AS', 'nM', 'GX', 'GN', 'CB', 'UB'] |
name: value name: value name: value name: value name: value |
filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf pbmc_1k_v2_L001.R1.10k.fastq.gz pbmc_1k_v2_L001.R2.10k.fastq.gz filtered.barcodes.txt value |
| Test-10 |
refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz refGenomeSource|genomeSAindexNbases: 4 refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf refGenomeSource|sjdbOverhang: 100 refGenomeSource|geneSource: history sc|input_types|input1: pbmc_1k_v2_L001.R1.10k.fastq.gz sc|input_types|input2: pbmc_1k_v2_L001.R2.10k.fastq.gz sc|input_types|use: repeat sc|soloCBwhitelist: filtered.barcodes.txt sc|params|chemistry: Cv3 sc|umidedup|soloUMIfiltering: MultiGeneUMI sc|umidedup|soloUMIdedup: 1MM_CR sc|soloCBmatchWLtype: 1MM_multi_pseudocounts sc|solo_type: CB_UMI_Simple solo|soloStrand: Forward solo|soloFeatures: GeneFull_ExonOverIntron solo|filter|filter_type: no_filter solo|soloOutFormatFeaturesGeneField3: Dummy Text |
name: value name: value name: value |
filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf pbmc_1k_v2_L001.R1.10k.fastq.gz pbmc_1k_v2_L001.R2.10k.fastq.gz filtered.barcodes.txt value |
| Test-11 |
refGenomeSource|GTFconditional|genomeDir: 000 refGenomeSource|GTFconditional|sjdbGTFfile: test1.gtf refGenomeSource|GTFconditional|sjdbOverhang: 75 refGenomeSource|GTFconditional|GTFselect: without-gtf-with-gtf refGenomeSource|geneSource: indexed sc|input_types|input1: pbmc_1k_v2_L001.R1.10k.fastq.gz sc|input_types|input2: pbmc_1k_v2_L001.R2.10k.fastq.gz sc|input_types|use: repeat sc|soloCBwhitelist: filtered.barcodes.txt sc|params|chemistry: Cv3 sc|umidedup|soloUMIdedup: 1MM_All sc|solo_type: CB_UMI_Simple solo|soloStrand: Forward solo|soloFeatures: Gene solo|filter|filter_type: no_filter solo|quantModeGene: True |
name: value name: value name: value name: value name: value name: value |
test1.gtf pbmc_1k_v2_L001.R1.10k.fastq.gz pbmc_1k_v2_L001.R2.10k.fastq.gz filtered.barcodes.txt value |
| Test-12 |
refGenomeSource|genomeFastaFiles: filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz refGenomeSource|genomeSAindexNbases: 4 refGenomeSource|sjdbGTFfile: filtered3.Homo_sapiens.GRCh38.100.chr21.gtf refGenomeSource|sjdbOverhang: 100 refGenomeSource|geneSource: history sc|input_types|input1: pbmc_1k_v2_L001.R1.10k.fastq.gz sc|input_types|input2: pbmc_1k_v2_L001.R2.10k.fastq.gz sc|input_types|use: repeat sc|soloCBwhitelist: filtered.barcodes.txt sc|params|chemistry: Cv3 sc|umidedup|soloUMIdedup: 1MM_All sc|solo_type: CB_UMI_Simple solo|soloStrand: Forward solo|soloFeatures: Gene Velocyto solo|filter|filter_type: no_filter solo|quantModeGene: True |
name: value name: value name: value name: value name: value |
filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz filtered3.Homo_sapiens.GRCh38.100.chr21.gtf pbmc_1k_v2_L001.R1.10k.fastq.gz pbmc_1k_v2_L001.R2.10k.fastq.gz filtered.barcodes.txt value |