Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/scpipe/scpipe/1.0.0+galaxy2 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/scpipe/scpipe/1.0.0+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/scpipe/scpipe/1.0.0 |
scpipe |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
bioconductor-scpipe | 1.0.0 | package |
bioconductor-rsubread | 1.28.1 | package |
bioconductor-rhtslib | 1.10.0 | package |
r-knitr | 1.20 | package |
r-rmarkdown | 1.10 | package |
r-readr | 1.1.1 | package |
r-plotly | 4.7.1 | package |
r-dt | 0.4 | package |
bioconductor-scater | 1.6.0 | package |
bioconductor-scran | 1.6.2 | package |
r-rtsne | 0.13 | package |
r-ggplot2 | 2.2.1 | package |
r-optparse | 1.6.0 | package |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
samples|ref_fasta|ref_fa_hist: mm10_MT19.fa.gz samples|ref_fasta|fasta_source: history samples|paired_format|in1: CB51_MT19_R1.gz samples|paired_format|in2: CB51_MT19_R2.gz samples|paired_format|paired_format_selector: paired samples|format_select: fastq exons: mm10_MT19.gff3.gz organism: mmusculus_gene_ensembl us: -1 out|report: True adv|f|max_reads: 5000000 adv|f|min_count: 100 |
name: value name: value |
mm10_MT19.fa.gz CB51_MT19_R1.gz CB51_MT19_R2.gz mm10_MT19.gff3.gz value |
Test-2 |
samples|ref_fasta|fasta_source: cached samples|paired_format|in1: CB51_MT19_R1.gz samples|paired_format|in2: CB51_MT19_R2.gz samples|paired_format|paired_format_selector: paired samples|format_select: fastq exons: mm10_MT19.gff3.gz organism: mmusculus_gene_ensembl us: -1 adv|f|max_reads: 5000000 adv|f|min_count: 100 |
name: value |
CB51_MT19_R1.gz CB51_MT19_R2.gz mm10_MT19.gff3.gz value |
Test-3 |
samples|bam: aligned.mapped.bam samples|barcodes: barcode_anno.tsv samples|format_select: bam exons: mm10_MT19.gff3.gz organism: mmusculus_gene_ensembl us: -1 |
name: value |
aligned.mapped.bam barcode_anno.tsv mm10_MT19.gff3.gz value |
Test-4 |
samples|bam: aligned.mapped.bam samples|barcodes: barcode_anno.tsv samples|format_select: bam exons: mm10_MT19.gff3.gz organism: mmusculus_gene_ensembl us: -1 out|plots: True out|metrics_matrix: True |
name: value name: value name: value |
aligned.mapped.bam barcode_anno.tsv mm10_MT19.gff3.gz value |