dropletutils: dropletutils.xml annotate

annotate dropletutils.xml @ 8:0897e5d845c4 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 9d465ee72398a8a74fe499a2e4b74f507a5845cc"

author	iuc
date	Mon, 05 Jul 2021 13:39:31 +0000
parents	da5ecdcfc9ee
children

rev	line source
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	1 <?xml version="1.0" encoding="utf-8"?>
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	2 <tool id="dropletutils" name="DropletUtils" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	3 <description>Utilities for handling droplet-based single-cell RNA-seq data</description>
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	4 <xrefs>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	5 <xref type="bio.tools">dropletutils</xref>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	6 </xrefs>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	7 <edam_topics>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	8 <edam_topic>topic_0203</edam_topic>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	9 <edam_topic>topic_3168</edam_topic>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	10 <edam_topic>topic_3170</edam_topic>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	11 <edam_topic>topic_3308</edam_topic>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	12 </edam_topics>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	13 <edam_operations>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	14 <edam_operation>operation_1812</edam_operation>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	15 <edam_operation>operation_3200</edam_operation>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	16 </edam_operations>
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	17 <macros>
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	18 <token name="@TOOL_VERSION@">1.10.0</token>
8 0897e5d845c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 9d465ee72398a8a74fe499a2e4b74f507a5845cc" iuc parents: 7 diff changeset	19 <token name="@VERSION_SUFFIX@">2</token>
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	20 <token name="@TXIN@">tenx.input</token>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	21 <token name="@TXOUT@">tenx.output</token>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	22 <xml name="test_dirin" >
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	23 <conditional name="tenx_format">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	24 <param name="use" value="directory" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	25 <param name="input" value="in_matrix.mtx" />
3 2bbf0052aaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d" iuc parents: 2 diff changeset	26 <param name="input_barcodes" value="in_barcodes.tsv" />
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	27 <param name="input_genes" value="in_genes.tsv" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	28 </conditional>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	29 </xml>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	30 </macros>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	31 <requirements>
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	32 <requirement type="package" version="@TOOL_VERSION@">bioconductor-dropletutils</requirement>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	33 <requirement type="package" version="1.18.0" >bioconductor-scater</requirement>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	34 <requirement type="package" version="4.0">r-base</requirement>
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	35 <requirement type="package" version="1.2_18">r-matrix</requirement>
4 a75b34ff05f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 49840f36c6623746bb7f8eb64bf4bf0cdae9c24e" iuc parents: 3 diff changeset	36 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	37 </requirements>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	38 <version_command><![CDATA[
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	39 Rscript -e 'packageVersion("DropletUtils")' \| grep -oP '\d\.\d\.\d'
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	40 ]]>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	41 </version_command>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	42 <command detect_errors='exit_code'><![CDATA[
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	43 #if str($tenx_format.use) == 'directory':
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	44 mkdir '@TXIN@' &&
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	45 ln -s '$tenx_format.input' '@TXIN@/matrix.mtx' &&
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	46 ln -s '$tenx_format.input_genes' '@TXIN@/genes.tsv' &&
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	47 ln -s '$tenx_format.input_barcodes' '@TXIN@/barcodes.tsv' &&
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	48 #end if
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	49
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	50 #if str($operation.use) == 'filter':
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	51 #if str($operation.outformat) == 'directory':
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	52 mkdir '@TXOUT@' &&
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	53 #end if
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	54 #end if
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	55
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	56 Rscript '$__tool_directory__/scripts/dropletutils.Rscript' '$droplet_conf'
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	57 ]]>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	58 </command>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	59 <configfiles>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	60 <configfile name="droplet_conf" >
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	61 ## defaults
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	62 empty_fdr_threshold = 0.01
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	63 eparams = formals(emptyDrops)
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	64 dparams = formals(defaultDrops)
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	65 bparams = formals(barcodeRanks)
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	66
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	67 ## File params
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	68 intype='$tenx_format.use'
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	69 outtype=NULL
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	70
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	71 files=list()
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	72 files\$table='$table'
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	73 files\$plot='$plot'
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	74 files\$out=NULL
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	75
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	76 #if str($tenx_format.use) == 'directory':
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	77 files\$infile='@TXIN@'
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	78 #else
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	79 files\$infile='$input'
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	80 #end if
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	81
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	82 #if str($operation.use) == 'filter':
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	83 #if str($operation.method.use) == 'defaultdrops':
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	84 do.method="defaultDrops"
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	85 dparams\$expected=as.integer('$operation.method.expected')
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	86 dparams\$upper.quant=as.numeric('$operation.method.upperquant')
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	87 dparams\$lower.prop=as.numeric('$operation.method.lowerprop')
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	88 #else if str($operation.method.use) == 'emptydrops':
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	89 do.method="emptyDrops"
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	90 eparams\$lower=as.integer('$operation.method.lower')
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	91 empty_fdr_threshold=as.numeric('$operation.method.fdr_thresh')
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	92 #end if
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	93
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	94 outtype='$operation.outformat'
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	95 #if str($operation.outformat) == 'directory':
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	96 files\$out='@TXOUT@'
5 d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	97 #else if str($operation.outformat) == 'h5':
d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	98 files\$out='$fileout_h5'
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	99 #else if str($operation.outformat) == 'tsv':
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	100 files\$out='$fileout_tsv'
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	101 #end if
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	102
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	103 #else if str($operation.use) == 'barcode_rank':
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	104 do.method="barcodeRankings"
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	105 bparams\$lower=as.integer('$operation.lower')
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	106 #end if
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	107
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	108 seed.val=as.integer('$seed')
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	109
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	110 </configfile>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	111 </configfiles>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	112 <inputs>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	113 <conditional name="tenx_format">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	114 <param name="use" type="select" label="Format for the input matrix">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	115 <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option>
5 d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	116 <option value="h5" selected="true" >H5</option>
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	117 <option value="tsv">Tabular</option>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	118 </param>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	119 <when value="directory">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	120 <param name="input" type="data" format="mtx,txt" label="Count Data"/>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	121 <param name="input_genes" type="data" format="tabular,tsv,txt" label="Genes List"/>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	122 <param name="input_barcodes" type="data" format="tabular,tsv,txt" label="Barcodes List"/>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	123 </when>
5 d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	124 <when value="h5">
d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	125 <param name="input" type="data" format="h5" label="Count Data"/>
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	126 </when>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	127 <when value="tsv">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	128 <param name="input" type="data" format="tabular,tsv" label="Count Data" help="The first column must contain gene names, and the first row must contain barcode identifiers." />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	129 </when>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	130 </conditional>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	131 <conditional name="operation" >
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	132 <param name="use" type="select" label="Operation" help="The filtering uses intelligent methods to generate output 10X matrices as would be otherwise generated by CellRanger. The ranking option serves to illustrate the number of detected barcodes in the sample.">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	133 <option value="filter" selected="true">Filter for Barcodes</option>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	134 <option value="barcode_rank">Rank Barcodes</option>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	135 </param>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	136 <when value="filter">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	137 <conditional name="method">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	138 <param name="use" type="select" label="Method" help="The DefaultDrops method calls cells according to the number of UMIs associated with each barcode as implemented by CellRanger. The EmptyDrops method identifies empty droplets using a smart ambient background model." >
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	139 <option value="defaultdrops" selected="true">DefaultDrops</option>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	140 <option value="emptydrops">EmptyDrops</option>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	141 </param>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	142 <when value="defaultdrops">
2 58105e5efa8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b" iuc parents: 1 diff changeset	143 <param name="expected" type="integer" min="1" value="3000" label="Expected Number of Cells" help="The expected number of cells in the sample." />
58105e5efa8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b" iuc parents: 1 diff changeset	144 <param name="upperquant" type="float" min="0" max="1.0" value="0.99" label="Upper Quantile" help="The quantile of the top expected barcodes to consider." />
58105e5efa8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b" iuc parents: 1 diff changeset	145 <param name="lowerprop" type="float" min="0" max="1.0" value="0.1" label="Lower Proportion" help="The fraction of molecules of the upper quantile that must be exceeded for a cell barcode to be detected." />
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	146 </when>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	147 <when value="emptydrops">
2 58105e5efa8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b" iuc parents: 1 diff changeset	148 <param name="lower" type="integer" min="1" value="100" label="Lower-bound Threshold" help="The lower-bound threshold of the total UMI count at which barcodes beneath this are assumed to be empty droplets." />
58105e5efa8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b" iuc parents: 1 diff changeset	149 <param name="fdr_thresh" type="float" min="0" max="1" value="0.01" label="FDR Threshold" help="False Discovery Rate threshold at which droplets with significant deviations from the ambient profile are detected at this threshold. If set to 0, the threshold is ignored." />
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	150 </when>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	151 </conditional>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	152 <param name="outformat" type="select" label="Format for output matrices">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	153 <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option>
5 d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	154 <option value="h5" selected="true" >H5</option>
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	155 <option value="tsv">Tabular</option>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	156 </param>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	157 </when>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	158 <when value="barcode_rank">
2 58105e5efa8d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b" iuc parents: 1 diff changeset	159 <param name="lower" type="integer" min="1" value="100" label="Lower Bound" help="Lower bound on the total UMI count, at or below which all barcodes are assumed to correspond to empty droplets."/>
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	160 </when>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	161 </conditional>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	162 <param name="seed" type="integer" value="100" label="Random Seed" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	163 </inputs>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	164 <outputs>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	165 <data name="fileout_tsv" format="tsv" label="${tool.name} Count Matrix on ${on_string}">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	166 <filter>operation['use']=='filter' and operation['outformat'] == 'tsv' </filter>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	167 </data>
5 d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	168 <data name="fileout_h5" format="h5" label="${tool.name} H5 Matrix on ${on_string}">
d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	169 <filter>operation['use']=='filter' and operation['outformat'] == 'h5'</filter>
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	170 </data>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	171 <data name="barcodes_out" format="tsv" from_work_dir="@TXOUT@/barcodes.tsv" label="${tool.name} 10X Barcodes on ${on_string}" >
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	172 <filter>operation['use']=='filter' and operation['outformat'] == 'directory'</filter>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	173 </data>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	174 <data name="genes_out" format="tsv" from_work_dir="@TXOUT@/genes.tsv" label="${tool.name} 10X Genes on ${on_string}" >
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	175 <filter>operation['use']=='filter' and operation['outformat'] == 'directory'</filter>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	176 </data>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	177 <data name="matrix_out" format="mtx" from_work_dir="@TXOUT@/matrix.mtx" label="${tool.name} 10X Matrices on ${on_string}" >
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	178 <filter>operation['use']=='filter' and operation['outformat'] == 'directory'</filter>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	179 </data>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	180 <data name="plot" format="png" label="${tool.name} Plot on ${on_string}">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	181 <filter>(operation['use']=='filter' and operation['method']['use']=="emptydrops") or operation['use']=='barcode_rank'</filter>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	182 </data>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	183 <data name="table" format="tsv" label="${tool.name} Table on ${on_string}">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	184 <filter>operation['use']=='filter' and operation['method']['use']=="emptydrops"</filter>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	185 </data>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	186 </outputs>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	187 <tests>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	188 <!-- Directory input tests -->
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	189 <test expect_num_outputs="1">
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	190 <!-- ::: Default Drops -->
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	191 <expand macro="test_dirin" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	192 <conditional name="operation">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	193 <param name="use" value="filter" />
5 d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	194 <param name="outformat" value="h5" /><!-- H5 -->
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	195 </conditional>
5 d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	196 <output name="fileout_h5" value="defs_defaultdrops.h5" compare="sim_size" delta="10" />
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	197 </test>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	198 <test expect_num_outputs="1">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	199 <expand macro="test_dirin" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	200 <conditional name="operation">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	201 <param name="use" value="filter" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	202 <param name="outformat" value="tsv" /><!-- TSV -->
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	203 </conditional>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	204 <output name="fileout_tsv" >
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	205 <assert_contents>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	206 <has_n_columns n="1026" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	207 <has_text_matching expression="^\sTCGCCAAGAA\sGGACTTAGAA\sTGCGCCTGAA\sACGGACACAA\sGCGGACACAA" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	208 <has_text_matching expression="GENE50\s4\s0\s0\s0\s0\s5\s11\s8\s5" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	209 <has_text_matching expression="GENE100\s6\s3\s5\s0\s0\s16\s31\s15\s26" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	210 </assert_contents>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	211 </output>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	212 </test>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	213 <test expect_num_outputs="1">
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	214 <!-- :: Barcode Ranks -->
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	215 <expand macro="test_dirin" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	216 <conditional name="operation">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	217 <param name="use" value="barcode_rank" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	218 <param name="lower" value="120" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	219 </conditional>
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	220 <output name="plot" value="defs_barcoderankings.png" compare="sim_size" delta="600"/>
8 0897e5d845c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 9d465ee72398a8a74fe499a2e4b74f507a5845cc" iuc parents: 7 diff changeset	221 <assert_stdout>
0897e5d845c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 9d465ee72398a8a74fe499a2e4b74f507a5845cc" iuc parents: 7 diff changeset	222 <has_line line='[1] "knee = 324 , inflection = 151"'/>
0897e5d845c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 9d465ee72398a8a74fe499a2e4b74f507a5845cc" iuc parents: 7 diff changeset	223 </assert_stdout>
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	224 </test>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	225 <test expect_num_outputs="3">
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	226 <!-- ::: Empty Drops -->
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	227 <expand macro="test_dirin" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	228 <conditional name="operation">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	229 <param name="use" value="filter" />
5 d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	230 <param name="outformat" value="h5" />
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	231 <conditional name="method">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	232 <param name="use" value="emptydrops" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	233 <param name="lower" value="150" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	234 <param name="fdr_thresh" value="0.02" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	235 </conditional>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	236 </conditional>
5 d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	237 <output name="fileout_h5" value="defs_emptydrops_150_0002.h5" compare="sim_size" delta="10" />
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	238 <output name="table" >
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	239 <assert_contents>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	240 <has_n_columns n="9" />
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	241 <has_line_matching expression="^\sbar_names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis_cell\sis_cellandlimited" />
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	242 <has_line_matching expression="^994\sGGCATTACAA\s338\s-246\.(.*TRUE){3}$" />
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	243 <has_line_matching expression="^998\sCATGAAGCAA\s151\s-166\.(.*TRUE){3}$" />
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	244 </assert_contents>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	245 </output>
4 a75b34ff05f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 49840f36c6623746bb7f8eb64bf4bf0cdae9c24e" iuc parents: 3 diff changeset	246 <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="400" />
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	247 </test>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	248 <!-- Other format input tests -->
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	249 <test expect_num_outputs="3">
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	250 <!-- ::: Empty Drops, same as above but input is h5 -->
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	251 <conditional name="tenx_format" >
5 d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	252 <param name="use" value="h5" />
d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	253 <param name="input" value="in_matrix.h5" />
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	254 </conditional>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	255 <conditional name="operation">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	256 <param name="use" value="filter" />
5 d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	257 <param name="outformat" value="h5" />
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	258 <conditional name="method">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	259 <param name="use" value="emptydrops" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	260 <param name="lower" value="150" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	261 <param name="fdr_thresh" value="0.02" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	262 </conditional>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	263 </conditional>
5 d5e4b59d5331 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7" iuc parents: 4 diff changeset	264 <output name="fileout_h5" value="defs_emptydrops_150_0002a.h5" compare="sim_size" delta="400" />
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	265 <output name="table" >
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	266 <assert_contents>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	267 <has_n_columns n="9" />
6 a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	268 <has_line_matching expression="^\sbar_names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis_cell\sis_cellandlimited" />
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	269 <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198\.(.*TRUE){3}$" />
a79cf05ca77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738" iuc parents: 5 diff changeset	270 <has_line_matching expression="^1114\sTCCGAAGCAA\s182\s-196\.(.*TRUE){3}$" />
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	271 </assert_contents>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	272 </output>
4 a75b34ff05f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 49840f36c6623746bb7f8eb64bf4bf0cdae9c24e" iuc parents: 3 diff changeset	273 <output name="plot" value="defs_emptydrops_150_0002a.png" compare="sim_size" delta="400" />
0 1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	274 </test>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	275 <!-- Output a directory -->
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	276 <test expect_num_outputs="3">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	277 <conditional name="tenx_format" >
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	278 <param name="use" value="tsv" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	279 <param name="input" value="in_matrix.tsv" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	280 </conditional>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	281 <conditional name="operation">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	282 <param name="use" value="filter" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	283 <param name="outformat" value="directory" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	284 <conditional name="method">
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	285 <param name="use" value="defaultdrops" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	286 <param name="expected" value="2000" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	287 <param name="upperquant" value="0.85" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	288 <param name="lowerpopr" value="0.2" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	289 </conditional>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	290 </conditional>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	291 <output name="genes_out" file="in_genes.tsv" ftype="tsv" /><!-- same as the input in this case -->
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	292 <output name="barcodes_out" ftype="tsv" >
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	293 <assert_contents>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	294 <has_n_columns n="1" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	295 <has_line line="GGAAGAAGAA" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	296 <has_line line="TCGAATGGAA" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	297 </assert_contents>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	298 </output>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	299 <output name="matrix_out" ftype="mtx" >
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	300 <assert_contents>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	301 <has_line_matching expression="^100\s2650\s64072$" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	302 <has_line_matching expression="^19\s1\s1$" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	303 <has_line_matching expression="^100\s2650\s1$" />
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	304 </assert_contents>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	305 </output>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	306 </test>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	307 </tests>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	308 <help><![CDATA[
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	309 Utilities to process 10X data in a variety of formats. Methods include:
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	310
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	311 Filter data:
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	312
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	313 * DefaultDrops emulates the native 10X method to produce a filtered count matrix
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	314 * EmptyDrops is a more informative quantile-based approach to produce a filtered count matrix.
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	315
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	316 Metrics:
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	317
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	318 * RankBarcodes produces a gap statistic plot to estimate the number of barcodes detected in the sample matrix.
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	319
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	320 Background
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	321
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	322 Droplet-based single-cell RNA sequencing (scRNA-seq) technologies allow researchers to obtain transcriptome-wide expression profiles for thousands of cells at once. Briefly, each cell is encapsulated in a droplet in a oil-water emulsion, along with a bead containing reverse transcription primers with a unique barcode sequence. After reverse transcription inside the droplet, each cell’s cDNA is labelled with that barcode (referred to a “cell barcode”). Bursting of the droplets yields a pool of cDNA for library preparation and sequencing. Debarcoding of the sequences can then be performed to obtain the expression profile for each cell.
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	323
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	324 This tool implements some general utilities for handling these data after quantification of expression. In particular, we focus on the 10X Genomics platform, providing functions to load in the matrix of unique molecule identifier (UMI) counts as well as the raw molecule information. Functions are also available for downsampling the UMI count matrix or the raw reads; for distinguishing cells from empty droplets, based on the UMI counts; and to eliminate the effects of barcode swapping on Illumina 4000 sequencing machine.
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	325 ]]></help>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	326 <citations>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	327 <citation type="doi">10.1186/s13059-019-1662-y</citation>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	328 </citations>
1335bf5bcd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7 iuc parents: diff changeset	329 </tool>

Mercurial > repos > iuc > dropletutils

annotate dropletutils.xml @ 8:0897e5d845c4 draft default tip