scpipe: scpipe.xml annotate

annotate scpipe.xml @ 4:3ffca09599ca draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7"

author	iuc
date	Fri, 16 Oct 2020 14:38:33 +0000
parents	5c4bca9dd4a2
children	a3b3ec00bf8f

rev	line source
4 3ffca09599ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7" iuc parents: 2 diff changeset	1 <tool id="scpipe" name="scPipe" version="1.0.0+galaxy2" profile="19.01">
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	2 <description>- preprocessing pipeline for single cell RNA-seq</description>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	3 <requirements>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	4 <requirement type="package" version="1.0.0">bioconductor-scpipe</requirement>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	5 <requirement type="package" version="1.28.1">bioconductor-rsubread</requirement>
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	6 <!-- rhtslib can be removed with a newer scpipe package -->
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	7 <requirement type="package" version="1.10.0">bioconductor-rhtslib</requirement>
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	8 <requirement type="package" version="1.20">r-knitr</requirement>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	9 <requirement type="package" version="1.10">r-rmarkdown</requirement>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	10 <requirement type="package" version="1.1.1">r-readr</requirement>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	11 <requirement type="package" version="4.7.1">r-plotly</requirement>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	12 <requirement type="package" version="0.4">r-dt</requirement>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	13 <requirement type="package" version="1.6.0">bioconductor-scater</requirement>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	14 <requirement type="package" version="1.6.2">bioconductor-scran</requirement>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	15 <requirement type="package" version="0.13">r-rtsne</requirement>
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	16 <!-- Using older version of ggplot2 as getting error like this with 3.0.0:
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	17 https://github.com/ggobi/ggally/issues/263 -->
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	18 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	19 <requirement type="package" version="1.6.0">r-optparse</requirement>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	20 </requirements>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	21 <version_command><![CDATA[
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	22 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: ")
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	23 ]]></version_command>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	24 <command detect_errors="exit_code"><![CDATA[
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	25 #import re
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	26
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	27 ## Link input files
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	28
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	29 #if $samples.format_select == "bam":
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	30 #set $bam_name = re.sub('[^\w\-\s]', '_', str($samples.bam.element_identifier))
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	31 ln -s '$samples.bam' '$bam_name' &&
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	32 ln -s '$samples.bam.metadata.bam_index' '${bam_name}.bai' &&
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	33 #else:
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	34
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	35 ## FASTA ##
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	36
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	37 #if $samples.ref_fasta.fasta_source == "history":
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	38 #set $fasta_name = re.sub('[^\w\-\s]', '_', str($samples.ref_fasta.ref_fa_hist.element_identifier))
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	39 ln -s '$samples.ref_fasta.ref_fa_hist' '$fasta_name' &&
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	40 #else:
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	41 #set $fasta_name = os.path.basename(str($samples.ref_fasta.ref_fa_builtin.fields.path))
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	42 ln -s '$samples.ref_fasta.ref_fa_builtin.fields.path' '$fasta_name' &&
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	43 #end if
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	44
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	45 ## Reads ##
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	46
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	47 #if $samples.paired_format.paired_format_selector == 'paired_collection':
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	48 #set $in1 = $samples.paired_format.paired_input.forward
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	49 #set $in2 = $samples.paired_format.paired_input.reverse
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	50 #set $in1_name = re.sub('[^\w\-\s]', '_', str($samples.paired_format.paired_input.name))
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	51 #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_%s" % ($samples.paired_format.paired_input.name, "R2")))
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	52 ln -s '$in1' '$in1_name' &&
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	53 ln -s '$in2' '$in2_name' &&
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	54 #elif $samples.paired_format.paired_format_selector == 'paired':
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	55 #set $in1 = $samples.paired_format.in1
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	56 #set $in2 = $samples.paired_format.in2
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	57 #set $in1_name = re.sub('[^\w\-\s]', '_', str($samples.paired_format.in1.element_identifier))
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	58 #set $in2_name = re.sub('[^\w\-\s]', '_', str($samples.paired_format.in2.element_identifier))
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	59 ln -s '$in1' '$in1_name' &&
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	60 ln -s '$in2' '$in2_name' &&
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	61 #end if
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	62 #end if
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	63
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	64 ## GFF3 ##
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	65
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	66 #set $anno_name = re.sub('[^\w\-\s]', '_', str($exons.element_identifier))
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	67 #set $anno_name = $anno_name + ".gff3"
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	68 ln -s '${exons}' '$anno_name' &&
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	69
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	70 #if $out.rscript:
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	71 cp '$__tool_directory__/scpipe.R' '$out_rscript' &&
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	72 #end if
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	73
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	74 TAB=\$(printf '\t') &&
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	75
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	76 #if $samples.barcodes:
4 3ffca09599ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7" iuc parents: 2 diff changeset	77 sed -e "s/\${TAB}/,/g" '$samples.barcodes' > samples.barcodes &&
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	78 #end if
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	79
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	80 ## Run scPipe
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	81
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	82 Rscript '$__tool_directory__/scpipe.R'
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	83
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	84 #if $samples.format_select == "bam":
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	85 --bam '$bam_name'
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	86 --samplename '$bam_name'
4 3ffca09599ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7" iuc parents: 2 diff changeset	87 --barcodes 'samples.barcodes'
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	88 #else:
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	89 --fasta '$fasta_name'
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	90 --read1 '$in1_name'
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	91 --read2 '$in2_name'
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	92 --samplename '$in1_name'
4 3ffca09599ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7" iuc parents: 2 diff changeset	93 #if $samples.barcodes:
3ffca09599ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7" iuc parents: 2 diff changeset	94 --barcodes 'samples.barcodes'
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	95 #end if
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	96 #end if
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	97
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	98 --exons '$anno_name'
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	99 --organism '$organism'
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	100
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	101 --bs1 $bs1
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	102 --bl1 $bl1
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	103 --bs2 $bs2
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	104 --bl2 $bl2
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	105 --us $us
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	106 --ul $ul
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	107
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	108 #if $out.metrics_matrix:
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	109 --metrics_matrix '$out.metrics_matrix'
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	110 #end if
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	111
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	112 #if $out.report:
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	113 --report '$out.report'
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	114 #end if
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	115
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	116 #if $out.rdata:
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	117 --rdata '$out.rdata'
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	118 #end if
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	119
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	120 --rmlow $adv.f.rmlow
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	121 --rmN $adv.f.rmN
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	122 --minq $adv.f.minq
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	123 --numbq $adv.f.numbq
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	124 --max_mis $adv.f.max_mis
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	125 --max_reads $adv.f.max_reads
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	126 --min_count $adv.f.min_count
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	127
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	128 --UMI_cor $adv.UMI_cor
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	129 --stnd $adv.stnd
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	130 --gene_fl $adv.gene_fl
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	131
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	132 --nthreads \${GALAXY_SLOTS:-2}
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	133
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	134 #if $keep_outliers:
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	135 --keep_outliers '$keep_outliers'
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	136 && sed -e "s/,/\${TAB}/g" gene_count.csv > gene_count.tsv
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	137 #end if
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	138
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	139 ]]></command>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	140
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	141 <inputs>
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	142 <conditional name="samples">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	143 <param name="format_select" type="select" label="FASTQs or BAM" help="Select the format of the input sample">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	144 <option value="fastq" selected="True">FASTQ</option>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	145 <option value="bam">BAM</option>
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	146 </param>
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	147 <when value="bam">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	148 <param name="bam" type="data" format="bam" label="BAM files"/>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	149 <param name="barcodes" type="data" format="tabular,tsv" label="Cell barcodes file" help="File of cell barcodes. Should contain at least two columns, where the first column has the cell id and the second column contains the barcode sequence."/>
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	150 </when>
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	151 <when value="fastq">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	152 <conditional name="ref_fasta">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	153 <param name="fasta_source" type="select" label="Reference genome FASTA">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	154 <option value="cached" selected="true">Use a built-in genome</option>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	155 <option value="history">Use a FASTA from history</option>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	156 </param>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	157 <when value="cached">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	158 <param name="ref_fa_builtin" type="select" label="Select a built-in FASTA" help="If your genome of interest is not listed, contact your Galaxy administrator">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	159 <options from_data_table="all_fasta">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	160 <filter type="sort_by" column="2" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	161 <validator type="no_options" message="No FASTA is available for the selected input dataset" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	162 </options>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	163 </param>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	164 </when>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	165 <when value="history">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	166 <param name="ref_fa_hist" type="data" format="fasta" label="Select a history FASTA" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	167 </when>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	168 </conditional>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	169 <conditional name="paired_format">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	170 <param name="paired_format_selector" type="select" label="Paired reads or Paired collection">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	171 <option value="paired">Paired</option>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	172 <option value="paired_collection">Paired Collection</option>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	173 </param>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	174 <when value="paired">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	175 <param name="in1" type="data" format="fastq.gz,fastq" label="Input Read 1" help="Read 1 should contain the transcripts in fastq.gz format"/>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	176 <param name="in2" type="data" format="fastq.gz,fastq" label="Input Read 2" help="Read 2 should contain UMI and barcodes in fastq.gz format"/>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	177 </when>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	178 <when value="paired_collection">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	179 <param name="paired_input" type="data_collection" collection_type="paired" format="fastq.gz,fastq" label="Select paired collection(s)"/>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	180 </when>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	181 </conditional>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	182 <param name="barcodes" type="data" format="tabular,tsv" optional="True" label="Cell barcodes file" help="Optional file of cell barcodes. If not provied the barcodes will be detected from the reads. Should contain at least two columns, where the first column has the cell id and the second column contains the barcode sequence."/>
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	183 </when>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	184 </conditional>
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	185 <param name="exons" type="data" format="gff3" label="Exon annotation GFF3 file" help="Current supported source is ENSEMBL"/>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	186 <param name="organism" type="text" label="Species gene id" help="This must be in biomaRt ENSEMBL listDatasets() format e.g. hsapiens_gene_ensembl. See the biomaRt user guide here: https://www.bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	187 <validator type="empty_field" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	188 <validator type="regex" message="Only letters and underscores are allowed">^[$\w$]+$</validator>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	189 </param>
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	190 <param argument="--bs1" type="integer" min="-1" value="-1" label="Barcode start Read 1" help="Barcode start position in Read 1. Positions are 0-indexed so the first base is considered base 0, -1 indicates no barcode. Default: -1" />
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	191 <param argument="--bl1" type="integer" min="0" value="0" label="Barcode length Read 1" help="Barcode length in Read 1, 0 if no barcode present. Default: 0" />
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	192 <param argument="--bs2" type="integer" min="-1" value="6" label="Barcode start Read 2" help="Barcode start position in Read 2. Positions are 0-indexed so the first base is considered base 0, -1 indicates no barcode. Default: 6" />
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	193 <param argument="--bl2" type="integer" min="0" value="8" label="Barcode length Read 2" help="Barcode length in Read 2, 0 if no barcode present. Default: 8" />
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	194 <param argument="--us" type="integer" min="-1" value="0" label="UMI start Read 2" help="UMI start position in Read 2. Positions are 0-indexed so the first base is considered base 0, -1 indicates no UMI. Default: 0" />
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	195 <param argument="--ul" type="integer" min="0" value="6" label="UMI length Read 2" help="UMI length in Read 2, 0 if no UMI present. Default: 6" />
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	196 <param name="keep_outliers" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Keep outliers?" help="If this option is set to Yes, outlier cells will not be removed from the gene count matrix. Default: No" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	197 <section name="out" title="Output Options">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	198 <param name="plots" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Output PDF with plots?" help="If this option is set to Yes, a PDF containing QC plots will be output. Default: Yes" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	199 <param name="metrics_matrix" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output QC metrics matrix?" help="If this option is set a matrix of QC metrics will be output. Default: No" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	200 <param name="report" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output HTML Report?" help="Only valid if FASTQs are input. If this option is set to Yes, a HTML report containing QC metrics will be output. Default: No" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	201 <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	202 <param name="rdata" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?"
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	203 help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	204 </param>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	205 </section>
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	206 <section name="adv" title="Advanced Options">
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	207 <section name="f" title="FASTQ input only">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	208 <param argument="--rmlow" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with N in barcode or UMI" help="Default: Yes" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	209 <param argument="--rmN" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with low quality" help="Default: Yes" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	210 <param argument="--minq" type="integer" min="0" value="20" label="Minimum read quality" help="Default: 20" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	211 <param argument="--numbq" type="integer" min="0" value="2" label="Maximum number of bases below minq" help="Default: 2" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	212 <param argument="--max_mis" type="integer" min="0" value="1" label="Maximum mismatch allowed in barcode" help="Default: 1" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	213
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	214 <param argument="--max_reads" type="integer" min="0" value="1000000" label="Maximum reads processed" help="Maximum reads processed if detecting barcodes. Default: 1,000,000" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	215 <param argument="--min_count" type="integer" min="0" value="10" label="Minimum count to keep" help="Minimum count to keep if detecting barcodes. Barcode will be discarded if it has lower count. This should be set according to --max_reads. Default: 10" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	216 </section>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	217 <param argument="--UMI_cor" type="integer" min="0" value="1" label="Correct UMI sequence error" help="0 means no correction, 1 means simple correction and merge UMI with distance 1. Default: 1" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	218 <param argument="--stnd" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Perform strand-specific mapping" help="Default: Yes" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	219 <param argument="--gene_fl" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Remove low abundant genes" help="Low abundant is defined as only one copy of one UMI for this gene. Default: No" />
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	220 </section>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	221 </inputs>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	222
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	223 <outputs>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	224 <data name="out_matrix" format="tabular" from_work_dir="gene_count.tsv" label="${tool.name} on ${on_string}: Count Matrix" />
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	225 <data name="out_plots" format="pdf" from_work_dir="plots.pdf" label="${tool.name} on ${on_string}: Plots">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	226 <filter>plots</filter>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	227 </data>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	228 <data name="out_metrics_matrix" format="tabular" from_work_dir="metrics_matrix.tsv" label="${tool.name} on ${on_string}: QC metrics matrix">
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	229 <filter>metrics_matrix</filter>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	230 </data>
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	231 <data name="out_report" format="html" from_work_dir="report.nb.html" label="${tool.name} on ${on_string}: HTML Report" >
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	232 <filter>report</filter>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	233 </data>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	234 <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript">
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	235 <filter>rscript</filter>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	236 </data>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	237 <data name="out_rdata" format="rdata" from_work_dir="scPipe_analysis.RData" label="${tool.name} on ${on_string}: RData file">
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	238 <filter>rdata</filter>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	239 </data>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	240 </outputs>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	241
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	242 <tests>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	243 <!-- Ensure outputs work -->
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	244 <test>
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	245 <param name="format_select" value="fastq" />
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	246 <param name="fasta_source" value="history"/>
4 3ffca09599ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7" iuc parents: 2 diff changeset	247 <param name="ref_fa_hist" ftype="fasta.gz" value="mm10_MT19.fa.gz"/>
3ffca09599ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7" iuc parents: 2 diff changeset	248 <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/>
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	249 <param name="organism" value="mmusculus_gene_ensembl"/>
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	250 <param name="paired_format_selector" value="paired" />
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	251 <param name="in1" ftype="fastqsanger.gz" value="CB51_MT19_R1.gz"/>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	252 <param name="in2" ftype="fastqsanger.gz" value="CB51_MT19_R2.gz"/>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	253 <param name="us" value="-1"/>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	254 <param name="max_reads" value="5000000"/>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	255 <param name="min_count" value="100"/>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	256 <param name="report" value="True" />
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	257 <output name="out_matrix" >
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	258 <assert_contents>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	259 <has_text text="ENSMUSG00000024940" />
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	260 </assert_contents>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	261 </output>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	262 <output name="out_report" >
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	263 <assert_contents>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	264 <has_text text="scPipe report for sample" />
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	265 </assert_contents>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	266 </output>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	267 </test>
1 4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	268 <!-- Ensure built-in fasta works -->
4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	269 <test>
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	270 <param name="format_select" value="fastq" />
1 4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	271 <param name="fasta_source" value="cached"/>
4 3ffca09599ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7" iuc parents: 2 diff changeset	272 <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/>
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	273 <param name="organism" value="mmusculus_gene_ensembl"/>
1 4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	274 <param name="paired_format_selector" value="paired" />
4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	275 <param name="in1" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R1.gz"/>
4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	276 <param name="in2" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R2.gz"/>
4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	277 <param name="us" value="-1"/>
4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	278 <param name="max_reads" value="5000000"/>
4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	279 <param name="min_count" value="100"/>
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	280 <output name="out_matrix" >
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	281 <assert_contents>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	282 <has_text text="ENSMUSG00000064351" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	283 </assert_contents>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	284 </output>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	285 </test>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	286 <!-- Ensure BAM input works -->
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	287 <test>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	288 <param name="format_select" value="bam" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	289 <param name="bam" ftype="bam" value="aligned.mapped.bam"/>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	290 <param name="barcodes" ftype="tabular" value="barcode_anno.tsv"/>
4 3ffca09599ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7" iuc parents: 2 diff changeset	291 <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/>
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	292 <param name="organism" value="mmusculus_gene_ensembl"/>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	293 <param name="us" value="-1"/>
1 4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	294 <output name="out_matrix" >
4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	295 <assert_contents>
4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	296 <has_text text="ENSMUSG00000064351" />
4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	297 </assert_contents>
4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	298 </output>
4ec6717872b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a iuc parents: 0 diff changeset	299 </test>
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	300 <!-- Ensure BAM input with QC outputs works -->
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	301 <test>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	302 <param name="format_select" value="bam" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	303 <param name="bam" ftype="bam" value="aligned.mapped.bam"/>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	304 <param name="barcodes" ftype="tabular" value="barcode_anno.tsv"/>
4 3ffca09599ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7" iuc parents: 2 diff changeset	305 <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/>
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	306 <param name="organism" value="mmusculus_gene_ensembl"/>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	307 <param name="us" value="-1"/>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	308 <param name="plots" value="True"/>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	309 <param name="metrics_matrix" value="True"/>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	310 <output name="out_matrix" >
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	311 <assert_contents>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	312 <has_text text="ENSMUSG00000064351" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	313 </assert_contents>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	314 </output>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	315 <output name="out_metrics_matrix" >
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	316 <assert_contents>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	317 <has_line_matching expression="cell_id.unaligned.aligned_unmapped.mapped_to_exon.mapped_to_intron.ambiguous_mapping.mapped_to_ERCC.mapped_to_MT.number_of_genes.total_count_per_cell.non_mt_percent\toutliers" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	318 </assert_contents>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	319 </output>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	320 <output name="out_plots" ftype="pdf" value="plots.pdf" compare="sim_size" />
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	321 </test>
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	322
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	323 </tests>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	324 <help><![CDATA[
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	325 .. class:: infomark
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	326
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	327 What it does
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	328
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	329 scPipe_ is an `R/Bioconductor package`_ that integrates barcode demultiplexing, read alignment, UMI-aware gene-level quantification and quality control of raw sequencing data generated by multiple protocols that include CEL-seq, MARS-seq, Chromium 10X, Drop-seq and Smart-seq. scPipe produces a count matrix that is essential for downstream analysis along with QC metrics and a HTML report that summarises data quality. These results can be used as input for downstream analyses including normalization, visualization and statistical testing.
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	330 The scPipe workflow is described in this vignette_ and examples of the report output can be found here_. Note that outlier cells are detected and removed by default but they can be kept if "Keep outliers?" is selected.
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	331
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	332 -----
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	333
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	334 Inputs
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	335
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	336 Either
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	337 * Reference genome in FASTA format
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	338 * Paired-end FASTQ.GZ reads
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	339 * Cell barcodes TAB-separated file (Optional)
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	340 OR
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	341 * BAM file
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	342 * Cell barcodes TAB-separated file
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	343 AND
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	344 * Exon annotation in ENSEMBL GFF3 format
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	345
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	346 Read Structure
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	347
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	348 The default read structure represents CEL-seq
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	349 paired-ended reads, with one cell barcode in Read 2 Start from
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	350 6bp and UMI sequence in Read 2 Start from the first bp. So the
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	351 read structure will be : `bs1=-1, bl1=0, bs2=6, bl2=8, us=0,
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	352 ul=6`. `bs1=-1, bl1=0` means we don't have index in Read 1 so we
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	353 set a negative value to start position and zero to the length.
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	354 `bs2=6, bl2=8` means we have index in Read 2 which starts at 6bp
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	355 with 8bp length. `us=0, ul=6` means we have UMI from the
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	356 start of Read 2 and the length is 6bp. NOTE: the zero
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	357 based index is used so the index of the sequence starts from zero. For a
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	358 typical Drop-seq experiment the setting will be `bs1=-1,
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	359 bl1=0, bs2=0, bl2=12, us=12, ul=8`, which means Read 1 only
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	360 contains transcript and the first 12bp in Read 2 are index,
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	361 followed by 8bp UMIs.
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	362
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	363 -----
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	364
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	365 Outputs
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	366
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	367 * Count matrix of genes in Tabular format
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	368
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	369 Optionally you can choose to output
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	370
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	371 * PDF of QC Plots (default is Yes)
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	372 * QC metrics matrix
5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	373 * HTML report (if FASTQs are input)
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	374 * Rscript
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	375 * RData
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	376
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	377 .. _scPipe: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006361
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	378 .. _R/Bioconductor package: https://bioconductor.org/packages/release/bioc/html/scPipe.html
2 5c4bca9dd4a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 60e2a9e9129a22924c55b11b218b39d913c7e686 iuc parents: 1 diff changeset	379 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/scPipe/inst/doc/scPipe_tutorial.html
0 32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	380 .. _here: http://bioinf.wehi.edu.au/scPipe/
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	381
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	382 ]]></help>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	383 <citations>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	384 <citation type="doi">10.1371/journal.pcbi.1006361</citation>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	385 </citations>
32e1bfc6b7b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7 iuc parents: diff changeset	386 </tool>

Mercurial > repos > iuc > scpipe

annotate scpipe.xml @ 4:3ffca09599ca draft