spacexr_cside: spacexr_cside.xml annotate

annotate spacexr_cside.xml @ 0:2b1797b4cbb1 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca

author	iuc
date	Tue, 28 Jan 2025 09:44:07 +0000
parents
children

rev	line source
0 2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	1 <tool id="spacexr_cside" name="CSIDE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	2 <description>Cell type-specific differential expression with C-SIDE</description>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	3 <macros>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	4 <import>macros.xml</import>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	5 </macros>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	6 <expand macro="edam"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	7 <expand macro="requirements">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	8 <requirement type="package" version="3.5.1">r-ggplot2</requirement>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	9 </expand>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	10 <command detect_errors="exit_code"><![CDATA[
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	11 export GALAXY_SLOTS=2 &&
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	12 mkdir -p 'inputs' 'results' 'logs' 'figures' &&
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	13 ln -s '$rctd' 'inputs/rctd.rds' &&
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	14 #if $type.de_type == 'point_density':
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	15 ln -s '$barcodes' 'inputs/barcodes.tabular' &&
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	16 #end if
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	17 #if $type.de_type == 'custom':
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	18 ln -s '$barcodes' 'inputs/barcodes.tabular' &&
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	19 #end if
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	20 touch 'results/cside_script.R' &&
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	21 cat '$cside_script' > 'results/cside_script.R' &&
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	22 Rscript 'results/cside_script.R'
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	23 ]]></command>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	24 <configfiles>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	25 <configfile name="cside_script"><![CDATA[
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	26 #if $type.cell_types != '':
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	27 #set $cell_types_list = ['"' + str(x.strip()) + '"' for x in str($type.cell_types).split(',')]
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	28 #set $cell_types = ','.join($cell_types_list)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	29 #end if
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	30 #if str($type.cell_types_present) != '':
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	31 #set $cell_types_present_list = ['"' + str(x.strip()) + '"' for x in str($type.cell_types_present).split(',')]
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	32 #set $cell_types_present = ','.join($cell_types_present_list)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	33 #end if
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	34 # cside script
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	35 # This file is used to specify the parameters for the cside from spacexr package
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	36
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	37 # Load the spacexr library
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	38 library('spacexr')
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	39 library('Matrix')
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	40 library('doParallel')
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	41
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	42 # load RCTD object
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	43 myRCTD <- readRDS('inputs/rctd.rds')
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	44
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	45 # set max cores
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	46 cores = Sys.getenv("GALAXY_SLOTS", unset= NA)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	47 if (is.na(cores) \|\| !nzchar(cores)) {
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	48 cores = 1
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	49 }
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	50 myRCTD@config[["max_cores"]] <- as.numeric(cores)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	51 print(paste("Using", cores, "cores"))
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	52
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	53 # CSIDE
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	54 #if str($type.de_type) == 'non_parametric':
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	55 myRCTD <- run.CSIDE.nonparam(myRCTD,
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	56 df = $type.df,
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	57 barcodes = NULL, # use all barcodes
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	58 CSIDE_COMMON_RUN
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	59 )
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	60
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	61 #else if str($type.de_type) == 'point_density':
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	62 barcodes <- read.delim('inputs/barcodes.tabular', header = FALSE, sep = '\t', check.names = FALSE)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	63 barcodes <- barcodes[,1]
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	64 pathogen_coords <- myRCTD@spatialRNA@coords[barcodes,]
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	65 barcodes <- colnames(myRCTD@spatialRNA@counts)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	66 explanatory.variable <- exvar.point.density(myRCTD,
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	67 barcodes,
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	68 pathogen_coords,
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	69 radius = $type.radius
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	70 )
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	71 CSIDE_SINGLE_RUN
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	72
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	73
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	74 #else if str($type.de_type) == 'cell2cell':
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	75 barcodes <- colnames(myRCTD@spatialRNA@counts)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	76 explanatory.variable <- exvar.celltocell.interactions(myRCTD,
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	77 barcodes,
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	78 '$type.cell_type',
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	79 radius = $type.radius
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	80 )
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	81 CSIDE_SINGLE_RUN
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	82
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	83
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	84 #else if str($type.de_type) == 'XY':
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	85 #if str($type.xy) == 'X':
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	86 explanatory.variable <- as.integer(myRCTD@spatialRNA@coords[['x']] > $type.lim)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	87 names(explanatory.variable) <- rownames(myRCTD@spatialRNA@coords)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	88
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	89 #else
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	90 explanatory.variable <- as.integer(myRCTD@spatialRNA@coords[['y']] > $type.lim)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	91 names(explanatory.variable) <- rownames(myRCTD@spatialRNA@coords)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	92 #end if
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	93 CSIDE_SINGLE_RUN
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	94
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	95 #else:
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	96 barcodes_df <- read.delim('inputs/barcodes.tabular', header = FALSE, sep = '\t', check.names = FALSE)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	97 region_list <- list()
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	98 for (i in 1:ncol(barcodes_df)) {
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	99 region <- barcodes_df[, i]
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	100 region <- region[region != "" & !is.na(region)]
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	101 region_list[[i]] <- region
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	102 }
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	103
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	104 myRCTD <- run.CSIDE.regions(myRCTD,
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	105 region_list,
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	106 log_fc_thresh = $type.log_FC_thresh,
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	107 CSIDE_COMMON_RUN
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	108 )
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	109 #end if
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	110
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	111
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	112 # save the results
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	113
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	114 # save significant genes in each cell type
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	115 cell_types <- names(myRCTD@de_results[["sig_gene_list"]])
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	116 for (cell_type in cell_types) {
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	117 df <- myRCTD@de_results[["sig_gene_list"]][[cell_type]]
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	118 assign(cell_type, df)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	119 write.table(df, file = paste0("results/", cell_type, "_sig.tabular"), sep = "\t", quote = FALSE)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	120 }
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	121 # save all genes in each cell type
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	122 cell_types <- names(myRCTD@de_results[["all_gene_list"]])
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	123 for (cell_type in cell_types) {
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	124 df <- myRCTD@de_results[["all_gene_list"]][[cell_type]]
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	125 assign(cell_type, df)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	126 write.table(df, file = paste0("results/", cell_type, ".tabular"), sep = "\t", quote = FALSE)
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	127 }
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	128
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	129 #if 'plots' in $output_selector:
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	130 # create plots
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	131 library('ggplot2')
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	132 make_all_de_plots(myRCTD, "figures")
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	133 #end if
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	134
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	135 #if 'rds' in $output_selector:
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	136 # save rds file
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	137 saveRDS(myRCTD, file = 'results/cside_results.rds')
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	138 #end if
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	139 ]]></configfile>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	140 </configfiles>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	141 <inputs>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	142 <param name="rctd" type="data" format="rds" label="RCTD object" help="annotated RCTD object"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	143 <conditional name="type">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	144 <param name="de_type" type="select" label="Type of covariates for explaining differential expression with C-SIDE">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	145 <option value="non_parametric">Smooth spatial pattern (non-non_parametric)</option>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	146 <option value="point_density">Proximity to pathology</option>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	147 <option value="cell2cell">Cell-to-cell interaction</option>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	148 <option value="XY">define X or Y axis</option>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	149 <option value="custom">Custom spatial locations</option>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	150 </param>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	151 <when value="non_parametric">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	152 <param argument="df" type="integer" min="0" value="15" label="Degrees of freedom" help="The degrees of freedom, or number of basis functions to be used in the model."/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	153 <expand macro="cside_common_input"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	154 </when>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	155 <when value="point_density">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	156 <expand macro="barcodes_input" label="One-column list of spatial barcodes" help="Only barcodes in first column will be used."/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	157 <expand macro="radius"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	158 <expand macro="cside_single_input"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	159 </when>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	160 <when value="cell2cell">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	161 <param name="cell_type" type="text" optional="false" label="Cell type for which to compute density">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	162 <expand macro="sanitizer"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	163 </param>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	164 <expand macro="radius"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	165 <expand macro="cside_single_input"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	166 </when>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	167 <when value="XY">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	168 <param name="lim" type="integer" value="" optional="false" label="Axis" help="The number on X or Y axis to discriminate two spatial regions"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	169 <param name="xy" type="boolean" truevalue="X" falsevalue="Y" checked="true" label="Is the number on X axis?"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	170 <expand macro="cside_single_input"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	171 </when>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	172 <when value="custom">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	173 <expand macro="barcodes_input" label="Tabular list of spatial barcodes" help="At least 3 regions should be specified"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	174 <expand macro="cside_common_input"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	175 <param argument="log_FC_thresh" type="float" min="0" value="0.4" label="logFC cutoff for differential expression"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	176 </when>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	177 </conditional>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	178 <expand macro="output">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	179 <option value="plots">DEG plots</option>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	180 <option value="log">log File</option>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	181 </expand>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	182 </inputs>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	183 <outputs>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	184 <collection name="de_results" type="list" label="${tool.name} on ${on_string}: DE Results">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	185 <discover_datasets pattern="(?P<name>.+)\.tabular$" format="tabular" directory="results"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	186 </collection>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	187 <collection name="de_plots" type="list" label="${tool.name} on ${on_string}: DE plots">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	188 <discover_datasets pattern="(?P<name>.+)\.pdf$" format="pdf" directory="figures/de_plots"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	189 <filter>output['output_selector'] and 'plots' in output['output_selector']</filter>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	190 </collection>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	191 <collection name="de_plots_quant" type="list" label="${tool.name} on ${on_string}: DE plots (quant)">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	192 <discover_datasets pattern="(?P<name>.+)\.pdf$" format="pdf" directory="figures/de_plots_quant"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	193 <filter>output['output_selector'] and 'plots' in output['output_selector']</filter>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	194 </collection>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	195 <collection name="de_plots_two_regions" type="list" label="${tool.name} on ${on_string}: DE plots (two regions)">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	196 <discover_datasets pattern="(?P<name>.+)\.pdf$" format="pdf" directory="figures/de_plots_two_regions"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	197 <filter>output['output_selector'] and 'plots' in output['output_selector']</filter>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	198 </collection>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	199 <data name="out_rds" format="rds" from_work_dir="results/cside_results.rds" label="${tool.name} on ${on_string}: RDS file">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	200 <filter>output['output_selector'] and 'rds' in output['output_selector']</filter>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	201 </data>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	202 <data name="out_rscript" format="txt" from_work_dir="results/cside_script.R" label="${tool.name} on ${on_string}: RScript">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	203 <filter>output['output_selector'] and 'rscript' in output['output_selector']</filter>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	204 </data>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	205 <data name="out_log" format="txt" from_work_dir="logs/de_log.txt" label="${tool.name} on ${on_string}: Log">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	206 <filter>output['output_selector'] and 'log' in output['output_selector']</filter>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	207 </data>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	208 </outputs>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	209 <tests>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	210 <!-- test non_parametric -->
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	211 <test expect_num_outputs="2">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	212 <param name="rctd" location="https://zenodo.org/records/14642119/files/myRCTD_merfish.rds"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	213 <param name="de_type" value="non_parametric"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	214 <param name="cell_types" value="Astrocytes"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	215 <param name="cell_type_threshold" value="10"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	216 <param name="gene_threshold" value="0.001"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	217 <param name="fdr" value="0.25"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	218 <param name="output_selector" value="rscript" />
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	219 <output_collection name="de_results" type="list">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	220 <element name="Astrocytes" ftype="tabular">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	221 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	222 <has_text_matching expression="Z_score.log_fc.se.paramindex_best.conv.*p_val"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	223 <has_text_matching expression="Gad1.3.8390[0-9].-3.6943[0-9].0.9623[0-9].6.TRUE.0.0017[0-9]"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	224 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	225 </element>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	226 <element name="Astrocytes_sig" ftype="tabular">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	227 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	228 <has_text_matching expression="Z_score.log_fc.se.paramindex_best.conv.*p_val"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	229 <has_text_matching expression="Glra3.3.9271[0-9].-7.2991[0-9].1.8586[0-9].8.TRUE.0.0012[0-9]"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	230 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	231 </element>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	232 </output_collection>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	233 <output name="out_rscript">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	234 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	235 <has_text_matching expression="run.CSIDE.nonparam"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	236 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	237 </output>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	238 </test>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	239 <!-- test fig and rds -->
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	240 <test expect_num_outputs="7">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	241 <param name="rctd" location="https://zenodo.org/records/14642119/files/myRCTD_merfish.rds"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	242 <param name="de_type" value="non_parametric"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	243 <param name="cell_types" value="Astrocytes"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	244 <param name="cell_type_threshold" value="10"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	245 <param name="gene_threshold" value="0.001"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	246 <param name="fdr" value="0.25"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	247 <param name="output_selector" value="rds,rscript,plots,log" />
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	248 <output_collection name="de_results" type="list">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	249 <element name="Astrocytes" ftype="tabular">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	250 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	251 <has_text_matching expression="Z_score.log_fc.se.paramindex_best.conv.*p_val"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	252 <has_text_matching expression="Gad1.3.8390[0-9].-3.6943[0-9].0.9623[0-9].6.TRUE.0.0017[0-9]"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	253 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	254 </element>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	255 <element name="Astrocytes_sig" ftype="tabular">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	256 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	257 <has_text_matching expression="Z_score.log_fc.se.paramindex_best.conv.*p_val"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	258 <has_text_matching expression="Glra3.3.9271[0-9].-7.2991[0-9].1.8586[0-9].8.TRUE.0.0012[0-9]"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	259 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	260 </element>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	261 </output_collection>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	262 <output_collection name="de_plots" type="list">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	263 <element name="de_genes_Astrocytes" location="https://zenodo.org/records/14642119/files/de_genes_Astrocytes.pdf" ftype="pdf" compare="sim_size"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	264 </output_collection>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	265 <output_collection name="de_plots_quant" type="list">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	266 <element name="de_genes_Astrocytes" location="https://zenodo.org/records/14642119/files/de_genes_Astrocytes_quant.pdf" ftype="pdf" compare="sim_size"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	267 </output_collection>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	268 <output_collection name="de_plots_two_regions" type="list">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	269 <element name="de_genes_Astrocytes" location="https://zenodo.org/records/14642119/files/de_genes_Astrocytes_two_regions" ftype="pdf" compare="sim_size"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	270 </output_collection>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	271 <output name="out_rds" location="https://zenodo.org/records/14642119/files/cside.rds" ftype="rds" compare="sim_size"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	272 <output name="out_rscript">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	273 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	274 <has_text_matching expression="run.CSIDE.nonparam"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	275 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	276 </output>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	277 <output name="out_log">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	278 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	279 <has_text_matching expression="Testing sample: 1 gene Rnd3"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	280 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	281 </output>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	282 </test>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	283 <!-- test point_density -->
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	284 <test expect_num_outputs="3">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	285 <param name="rctd" location="https://zenodo.org/records/14642119/files/myRCTD_merfish.rds"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	286 <param name="de_type" value="point_density"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	287 <param name="barcodes" location="https://zenodo.org/records/14642119/files/barcode.tabular"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	288 <param name="cell_types" value="Astrocytes"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	289 <param name="cell_type_threshold" value="10"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	290 <param name="gene_threshold" value="0.001"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	291 <param name="fdr" value="0.25"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	292 <param name="output_selector" value="rscript,log" />
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	293 <output_collection name="de_results" type="list">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	294 <element name="Astrocytes" ftype="tabular">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	295 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	296 <has_text_matching expression="Z_score.log_fc.se.paramindex_best.conv.p_val.mean_0.mean_1.sd_0.*sd_1"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	297 <has_text_matching expression="Gad1.0.0155[0-9].0.0088[0-9].0.5666[0-9].2.TRUE.0.9876[0-9].-4.9869[0-9].-4.9781[0-9].0.2504[0-9].0.5083[0-9]"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	298 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	299 </element>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	300 <element name="Astrocytes_sig" ftype="tabular">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	301 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	302 <has_text_matching expression="Z_score.log_fc.se.paramindex_best.conv.p_val.mean_0.mean_1.sd_0.*sd_1"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	303 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	304 </element>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	305 </output_collection>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	306 <output name="out_rscript">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	307 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	308 <has_text_matching expression="exvar.point.density"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	309 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	310 </output>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	311 <output name="out_log">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	312 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	313 <has_text_matching expression="Testing sample: 2 gene Gad1"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	314 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	315 </output>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	316 </test>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	317 <!-- test cell2cell -->
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	318 <test expect_num_outputs="3">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	319 <param name="rctd" location="https://zenodo.org/records/14642119/files/myRCTD_merfish.rds"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	320 <param name="de_type" value="cell2cell"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	321 <param name="cell_type" value="Excitatory"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	322 <param name="cell_types" value="Astrocytes"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	323 <param name="cell_type_threshold" value="10"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	324 <param name="gene_threshold" value="0.001"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	325 <param name="fdr" value="0.25"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	326 <param name="output_selector" value="rscript,log" />
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	327 <output_collection name="de_results" type="list">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	328 <element name="Astrocytes" ftype="tabular">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	329 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	330 <has_text_matching expression="Z_score.log_fc.se.paramindex_best.conv.p_val.mean_0.mean_1.sd_0.*sd_1"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	331 <has_text_matching expression="Gad1.1.2142[0-9].-0.9565[0-9].0.7877[0-9].2.TRUE.0.2246[0-9].-4.6413[0-9].-5.5978[0-9].0.3508[0-9].0.7053[0-9]"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	332 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	333 </element>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	334 <element name="Astrocytes_sig" ftype="tabular">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	335 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	336 <has_text_matching expression="Z_score.log_fc.se.paramindex_best.conv.p_val.mean_0.mean_1.sd_0.*sd_1"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	337 <has_text_matching expression="Pgr.3.6958[0-9].2.4095[0-9].0.6519[0-9].2.TRUE.0.0002[0-9].-7.2097[0-9].-4.8002[0-9].0.3666[0-9].0.5390[0-9]"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	338 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	339 </element>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	340 </output_collection>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	341 <output name="out_rscript">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	342 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	343 <has_text_matching expression="exvar.celltocell.interactions"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	344 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	345 </output>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	346 <output name="out_log">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	347 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	348 <has_text_matching expression="Testing sample: 1 gene Rnd3"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	349 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	350 </output>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	351 </test>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	352 <!-- test XY -->
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	353 <test expect_num_outputs="3">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	354 <param name="rctd" location="https://zenodo.org/records/14642119/files/myRCTD_merfish.rds"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	355 <param name="de_type" value="XY"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	356 <param name="lim" value="2000"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	357 <param name="xy" value="X"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	358 <param name="cell_types" value="Astrocytes"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	359 <param name="cell_type_threshold" value="10"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	360 <param name="gene_threshold" value="0.001"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	361 <param name="fdr" value="0.25"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	362 <param name="output_selector" value="rscript,log" />
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	363 <output_collection name="de_results" type="list">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	364 <element name="Astrocytes" ftype="tabular">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	365 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	366 <has_text_matching expression="Z_score.log_fc.se.paramindex_best.conv.p_val.mean_0.mean_1.sd_0.*sd_1"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	367 <has_text_matching expression="Gad1.0.7420[0-9].-0.3333[0-9].0.4492[0-9].2.TRUE.0.4580[0-9].-4.7997[0-9].-5.1331[0-9].0.3343[0-9].0.3000[0-9]"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	368 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	369 </element>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	370 <element name="Astrocytes_sig" ftype="tabular">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	371 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	372 <has_text_matching expression="Z_score.log_fc.se.paramindex_best.conv.p_val.mean_0.mean_1.sd_0.*sd_1"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	373 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	374 </element>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	375 </output_collection>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	376 <output name="out_rscript">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	377 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	378 <has_text_matching expression="explanatory\.variable <- as\.integer$myRCTD@spatialRNA@coords\[\['x'\]\] > 2000$"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	379 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	380 </output>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	381 <output name="out_log">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	382 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	383 <has_text_matching expression="Testing sample: 1 gene Rnd3"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	384 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	385 </output>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	386 </test>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	387 <!-- test custom -->
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	388 <test expect_num_outputs="3">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	389 <param name="rctd" location="https://zenodo.org/records/14642119/files/myRCTD_merfish.rds"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	390 <param name="de_type" value="custom"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	391 <param name="barcodes" location="https://zenodo.org/records/14642119/files/barcodes.tabular"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	392 <param name="cell_types" value="Inhibitory"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	393 <param name="cell_type_threshold" value="10"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	394 <param name="gene_threshold" value="0.001"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	395 <param name="cell_type_threshold" value="10"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	396 <param name="fdr" value="0.25"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	397 <param name="output_selector" value="rscript,log" />
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	398 <output_collection name="de_results" type="list">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	399 <element name="Inhibitory" ftype="tabular">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	400 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	401 <has_text_matching expression="sd_lfc.paramindex1_best.paramindex2_best.sd_best.p_val_best.log_fc_best.mean_1.mean_2.mean_3.sd_1.sd_2.*sd_3"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	402 <has_text_matching expression="Rnd3.0.0576[0-9].1.3.0.3116[0-9].1.0.1091[0-9].-5.1913[0-9].-5.1046[0-9].-5.0822[0-9].0.1963[0-9]"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	403 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	404 </element>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	405 <element name="Inhibitory_sig" ftype="tabular">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	406 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	407 <has_text_matching expression=""/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	408 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	409 </element>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	410 </output_collection>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	411 <output name="out_rscript">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	412 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	413 <has_text_matching expression="read\.delim\('inputs/barcodes\.tabular'"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	414 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	415 </output>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	416 <output name="out_log">
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	417 <assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	418 <has_text_matching expression="Testing sample: 1 gene Rnd3"/>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	419 </assert_contents>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	420 </output>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	421 </test>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	422 </tests>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	423 <help><![CDATA[
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	424
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	425 Cell type-Specific Inference of Differential Expression, or CSIDE, is part of the spacexr R package for learning cell type-specific differential expression from spatial transcriptomics data.
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	426
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	427 C-SIDE can detect differential expression (DE) along one or multiple user-defined axes, termed explanatory variables.
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	428
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	429 The user should first run RCTD on the data to annotated cell types. and use RCTD object rds file as input.
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	430
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	431 The explanatory variable (i.e. covariate) is used for predicting differential expression in CSIDE. In general one should set the explanatory variable to biologically relevant predictors of gene expression such as spatial position.
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	432
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	433 The explanatory variable can be defined in several ways:
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	434
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	435 * Smooth spatial pattern (non-parametric): This method uses a smooth spatial pattern to explain the differential expression.
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	436 * Proximity to pathology: This method uses the proximity to pathology (specific spatial locations) to explain the differential expression.
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	437 * Cell-to-cell interaction: This method uses the cell-to-cell interaction to explain the differential expression. The user should specify the cell type for which to compute density and the radius for the cell-to-cell interaction.
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	438 * Define X or Y axis: This method uses the X or Y axis to explain the differential expression. The user should specify the axis and the number on the axis to discriminate two spatial regions.
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	439 * Custom spatial locations: This method uses custom spatial locations to explain the differential expression. The user should specify at least 3 regions containing at least 2 spatial barcodes.
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	440 ]]></help>
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	441 <expand macro="citations" />
2b1797b4cbb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr commit c6f85f5bd2c9dee114640a4e4007852c060e10ca iuc parents: diff changeset	442 </tool>

Mercurial > repos > iuc > spacexr_cside

annotate spacexr_cside.xml @ 0:2b1797b4cbb1 draft default tip