Revision: 5:a3b3ec00bf8f

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/scpipe

Miscellaneous

Name: scPipe

Description: - preprocessing pipeline for single cell RNA-seq

Id: scpipe

Guid: toolshed.g2.bx.psu.edu/repos/iuc/scpipe/scpipe/1.0.0+galaxy2

Version: 1.0.0+galaxy2

Version command string: echo $(R --version | grep version | grep -v GNU)", scPipe version" $(R --vanilla --slave -e "library(scPipe); cat(sessionInfo()\$otherPkgs\$scPipe\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Rsubread version" $(R --vanilla --slave -e "library(Rsubread); cat(sessionInfo()\$otherPkgs\$Rsubread\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", knitr version" $(R --vanilla --slave -e "library(knitr); cat(sessionInfo()\$otherPkgs\$knitr\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rmarkdown version" $(R --vanilla --slave -e "library(rmarkdown); cat(sessionInfo()\$otherPkgs\$rmarkdown\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", readr version" $(R --vanilla --slave -e "library(readr); cat(sessionInfo()\$otherPkgs\$readr\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", plotly version" $(R --vanilla --slave -e "library(plotly); cat(sessionInfo()\$otherPkgs\$plotly\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", DT version" $(R --vanilla --slave -e "library(DT); cat(sessionInfo()\$otherPkgs\$DT\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scater version" $(R --vanilla --slave -e "library(scater); cat(sessionInfo()\$otherPkgs\$scater\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scran version" $(R --vanilla --slave -e "library(scran); cat(sessionInfo()\$otherPkgs\$scran\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rtsne version" $(R --vanilla --slave -e "library(Rtsne); cat(sessionInfo()\$otherPkgs\$Rtsne\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", ggplot2 version" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")

Display in tool panel: True

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)

Requirements:

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