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Commit message:
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6 |
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added:
extra/macro_mapper_seurat.yaml get_test_data.sh scripts/seurat-scale-data.R seurat_macros.xml seurat_plot.xml |
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| diff -r 000000000000 -r 95d79f1134f0 extra/macro_mapper_seurat.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extra/macro_mapper_seurat.yaml Sat Mar 02 10:40:08 2024 +0000 |
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| @@ -0,0 +1,90 @@ +--- +- option_group: + - input-object-file + - input-format + pre_command_macros: + - INPUT_OBJ_PREAMBLE + post_command_macros: + - INPUT_OBJECT + input_declaration_macros: + - input_object_params +- option_group: + - output-object-file + - output-format + post_command_macros: + - OUTPUT_OBJECT + input_declaration_macros: + - output_object_params + output_declaration_macros: + - output_files +- option_group: + - input-object-files + - input-format + pre_command_macros: + - INPUT_OBJS_PREAMBLE + post_command_macros: + - INPUT_OBJECTS + input_declaration_macros: + - input_object_params: + multiple: true +- option_group: + - reference-object-files + - reference-format + pre_command_macros: + - REFERENCE_OBJS_PREAMBLE + post_command_macros: + - REFERENCE_OBJECTS + input_declaration_macros: + - input_object_params: + varname: reference + multiple: true + optional: true +- option_group: + - reference-object-file + - reference-format + pre_command_macros: + - REFERENCE_OBJ_PREAMBLE + post_command_macros: + - REFERENCE_OBJECT + input_declaration_macros: + - input_object_params: + varname: reference +- option_group: + - anchors-object-file + - anchors-format + pre_command_macros: + - ANCHORS_OBJ_PREAMBLE + post_command_macros: + - ANCHORS_OBJECT + input_declaration_macros: + - input_object_params: + varname: anchors +- option_group: + - query-object-file + - query-format + pre_command_macros: + - QUERY_OBJ_PREAMBLE + post_command_macros: + - QUERY_OBJECT + input_declaration_macros: + - input_object_params: + varname: query +- option_group: + - plot-out + post_command_macros: + - OUTPUT_PLOT + output_declaration_macros: + - plot_output_files_format: + format: png + - plot_output_files_format: + format: pdf + - plot_output_files_format: + format: eps + - plot_output_files_format: + format: jpg + - plot_output_files_format: + format: ps + - plot_output_files_format: + format: tiff + - plot_output_files_format: + format: svg |
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| diff -r 000000000000 -r 95d79f1134f0 get_test_data.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_test_data.sh Sat Mar 02 10:40:08 2024 +0000 |
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| @@ -0,0 +1,77 @@ +#!/usr/bin/env bash + +BASENAME_FILE='E-MTAB-6077-3k_features_90_cells' + +MTX_LINK='https://drive.google.com/uc?export=download&id=1-1ejn7scP80xsbrG0FtWzsozjg0hhc23' +RDS_LINK='https://drive.google.com/uc?export=download&id=1KW_GX6xznSUpWRWUykpNaSbAhyClf7_n' +NORM_LINK='https://drive.google.com/uc?export=download&id=1mvo3ENkBvEAOyWG6ejApzQTPDLX5yBKU' +FVG_LINK='https://drive.google.com/uc?export=download&id=13Fhruuj-vEEo1WM138ahtAYqfHc7LsaZ' +SCALED_LINK='https://drive.google.com/uc?export=download&id=18TK8us235LWNajarWDBAtASUXMYAxvw0' +PCA_LINK='https://drive.google.com/uc?export=download&id=1gf3BTB4dygDsom1TzjsBfgZnZepcoG5c' +NEIGHBOURS_LINK='https://drive.google.com/uc?export=download&id=1N2lHoKRBZ7pmAYGfghLWB9KUrLA5WoNX' +CLUSTERS_LINK='https://drive.google.com/uc?export=download&id=1HWxZWHbNUNo4z__9PhhL_CJOLzec_ETa' +TSNE_LINK='https://drive.google.com/uc?export=download&id=1qsvMr_GkCSp1dyTJt1BZ6cElJwFFX2zO' +MARKERS_LINK='https://drive.google.com/uc?export=download&id=18OmWNc7mF-4pzH6DQkPp1eKunN4BfvxD' + +LOOM_LINK='https://drive.google.com/uc?export=download&id=1qNk5cg8hJG3Nv1ljTKmUEnxTOf11EEZX' +H5AD_LINK='https://drive.google.com/uc?export=download&id=1YpE0H_t_dkh17P-WBhPijKvRiGP0BlBz' + +H5AD_SC182_LINK='https://drive.google.com/uc?export=download&id=16PUJ2KAkXT8F1UkfqU-9LWoOJUkUG1rp' +SCE_LINK='https://drive.google.com/uc?export=download&id=1UKdyf3M01uAt7oBg93JfmRvNVB_jlUKe' + +# Seurat v4 exclusives +IFNB_BASE_FILE='ifnb_' + +IFNB_CTRL_INT_LINK='https://drive.google.com/uc?export=download&id=15E_MLz-UclJYInNaA7YKLhLo5W-qlykL' +IFNB_STIM_INT_LINK='https://drive.google.com/uc?export=download&id=14iKgCJGPk16dEmpJJF-Gp_lBDcOdo-54' + +## Classify and UMAP mapping +CLASSIFY_QUERY_LINK='https://oc.ebi.ac.uk/s/MlEDILFYRrvkS6E/download' +CLASSIFY_RESULTS_ANCHORS_OBJECT_LINK='https://drive.google.com/uc?export=download&id=1Xtv4K_CxIU1cJ8RjJ7NTvzLQkLvc8a3i' +# UMAP_RESULT_OBJECT_LINK='https://oc.ebi.ac.uk/s/k4MdM07y9DAnurp/download' +UMAP_RESULT_OBJECT_LINK='https://oc.ebi.ac.uk/s/D1z4z2ef1e3dyc3/download' + + +function get_data { + local link=$1 + local fname=$2 + + if [ ! -f $fname ]; then + echo "$fname not available locally, downloading.." + wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link + fi +} + +# get matrix data +mkdir -p test-data +pushd test-data +get_data $MTX_LINK mtx.zip +unzip mtx.zip +rm -f mtx.zip + +get_data $RDS_LINK $BASENAME_FILE".rds" +get_data $NORM_LINK $BASENAME_FILE"-normalised.rds" +get_data $FVG_LINK $BASENAME_FILE"-fvg.rds" +get_data $SCALED_LINK $BASENAME_FILE"-scaled.rds" +get_data $PCA_LINK $BASENAME_FILE"-pca.rds" +get_data $NEIGHBOURS_LINK $BASENAME_FILE"-neighbours.rds" +get_data $CLUSTERS_LINK $BASENAME_FILE"-clusters.rds" +get_data $TSNE_LINK $BASENAME_FILE"-tsne.rds" +get_data $MARKERS_LINK $BASENAME_FILE"-markers.csv.zip" + +unzip $BASENAME_FILE"-markers.csv.zip" +rm -f $BASENAME_FILE"-markers.csv.zip" + +get_data $LOOM_LINK $BASENAME_FILE"_loom.h5" +get_data $SCE_LINK $BASENAME_FILE"_sce.rds" +get_data $H5AD_LINK $BASENAME_FILE".h5ad" + +get_data $H5AD_SC182_LINK $BASENAME_FILE"_sc182.h5ad" + +get_data $IFNB_CTRL_INT_LINK $IFNB_BASE_FILE"ctrl_norm_fvg.rds" +get_data $IFNB_STIM_INT_LINK $IFNB_BASE_FILE"stim_norm_fvg.rds" + +get_data $CLASSIFY_QUERY_LINK "Classify_query.rds" +get_data $CLASSIFY_RESULTS_ANCHORS_OBJECT_LINK "Classify_anchors.rds" +get_data $UMAP_RESULT_OBJECT_LINK "UMAP_result_integrated.rds" + |
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| diff -r 000000000000 -r 95d79f1134f0 scripts/seurat-scale-data.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/seurat-scale-data.R Sat Mar 02 10:40:08 2024 +0000 |
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| @@ -0,0 +1,165 @@ +#!/usr/bin/env Rscript + +# Load optparse we need to check inputs + +suppressPackageStartupMessages(require(optparse)) + +# Load common functions + +suppressPackageStartupMessages(require(workflowscriptscommon)) + +# parse options + +option_list = list( + make_option( + c("-i", "--input-object-file"), + action = "store", + default = NA, + type = 'character', + help = "File name in which a serialized R matrix object may be found." + ), + make_option( + c("--input-format"), + action = "store", + default = "seurat", + type = 'character', + help = "Either loom, seurat, anndata or singlecellexperiment for the input format to read." + ), + make_option( + c("--output-format"), + action = "store", + default = "seurat", + type = 'character', + help = "Either loom, seurat, anndata or singlecellexperiment for the output format." + ), + make_option( + c("-e", "--genes-use"), + action = "store", + default = NULL, + type = 'character', + help = "File with gene names to scale/center (one gene per line). Default is all genes in object@data." + ), + make_option( + c("-v", "--vars-to-regress"), + action = "store", + default = NULL, + type = 'character', + help = "Comma-separated list of variables to regress out (previously latent.vars in RegressOut). For example, nUMI, or percent.mito." + ), + make_option( + c("-m", "--model-use"), + action = "store", + default = 'linear', + type = 'character', + help = "Use a linear model or generalized linear model (poisson, negative binomial) for the regression. Options are 'linear' (default), 'poisson', and 'negbinom'." + ), + make_option( + c("-u", "--use-umi"), + action = "store", + default = FALSE, + type = 'logical', + help = "Regress on UMI count data. Default is FALSE for linear modeling, but automatically set to TRUE if model.use is 'negbinom' or 'poisson'." + ), + make_option( + c("-s", "--do-not-scale"), + action = "store_true", + default = FALSE, + type = 'logical', + help = "Skip the data scale." + ), + make_option( + c("-c", "--do-not-center"), + action = "store_true", + default = FALSE, + type = 'logical', + help = "Skip data centering." + ), + make_option( + c("-x", "--scale-max"), + action = "store", + default = 10, + type = 'double', + help = "Max value to return for scaled data. The default is 10. Setting this can help reduce the effects of genes that are only expressed in a very small number of cells. If regressing out latent variables and using a non-linear model, the default is 50." + ), + make_option( + c("-b", "--block-size"), + action = "store", + default = 1000, + type = 'integer', + help = "Default size for number of genes to scale at in a single computation. Increasing block.size may speed up calculations but at an additional memory cost." + ), + make_option( + c("-d", "--min-cells-to-block"), + action = "store", + default = 1000, + type = 'integer', + help = "If object contains fewer than this number of cells, don't block for scaling calculations." + ), + make_option( + c("-n", "--check-for-norm"), + action = "store", + default = TRUE, + type = 'logical', + help = "Check to see if data has been normalized, if not, output a warning (TRUE by default)." + ), + make_option( + c("-o", "--output-object-file"), + action = "store", + default = NA, + type = 'character', + help = "File name in which to store serialized R object of type 'Seurat'.'" + ) +) + +opt <- wsc_parse_args(option_list, mandatory = c('input_object_file', 'output_object_file')) + +# Check parameter values + +if ( ! file.exists(opt$input_object_file)){ + stop((paste('File', opt$input_object_file, 'does not exist'))) +} + +if (! is.null(opt$genes_use)){ + if (! file.exists(opt$genes_use)){ + stop((paste('Supplied genes file', opt$genes_use, 'does not exist'))) + }else{ + genes_use <- readLines(opt$genes_use) + } +}else{ + genes_use <- NULL +} + +# break up opt$vars_to_regress into a list if it has commas +opt$vars_to_regress <- unlist(strsplit(opt$vars_to_regress, ",")) + +# Now we're hapy with the arguments, load Seurat and do the work + +suppressPackageStartupMessages(require(Seurat)) +if(opt$input_format == "loom" | opt$output_format == "loom") { + suppressPackageStartupMessages(require(SeuratDisk)) +} else if(opt$input_format == "singlecellexperiment" | opt$output_format == "singlecellexperiment") { + suppressPackageStartupMessages(require(scater)) +} + +# Input from serialized R object + +seurat_object <- read_seurat4_object(input_path = opt$input_object_file, format = opt$input_format) +# https://stackoverflow.com/questions/9129673/passing-list-of-named-parameters-to-function +# might be useful +scaled_seurat_object <- ScaleData(seurat_object, + features = genes_use, + vars.to.regress = opt$vars_to_regress, + model.use = opt$model_use, + use.umi = opt$use_umi, + do.scale = !opt$do_not_scale, + do.center = !opt$do_not_center, + scale.max = opt$scale_max, + block.size = opt$block_size, + min.cells.to.block = opt$min_cells_to_block, + verbose = FALSE) + + +# Output to a serialized R object +write_seurat4_object(seurat_object = scaled_seurat_object, + output_path = opt$output_object_file, + format = opt$output_format) |
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| diff -r 000000000000 -r 95d79f1134f0 seurat_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seurat_macros.xml Sat Mar 02 10:40:08 2024 +0000 |
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| b'@@ -0,0 +1,354 @@\n+<?xml version="1.0"?>\n+<macros>\n+ <token name="@VERSION@">4.0.0</token>\n+ <token name="@SEURAT_VERSION@">4.0.4</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">seurat-scripts</requirement>\n+ </requirements>\n+ </xml>\n+ <xml name="version">\n+ \t<version_command><![CDATA[\n+echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\\$otherPkgs\\$seurat\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\n+ ]]></version_command>\n+ </xml>\n+\n+ <xml name="input_object_params" token_multiple="False" token_varname="input" token_optional="False">\n+ <conditional name="@VARNAME@" label="Input format">\n+ <param type="select" name="format" label="Choose the format of the @VARNAME@" help="Seurat RDS, Seurat H5, Single Cell Experiment RDS, Loom or AnnData">\n+ <option value="rds_seurat" selected="true">RDS with a Seurat object</option>\n+ <option value="loom">Loom</option>\n+ <option value="h5seurat">Seurat HDF5</option>\n+ <option value="anndata">AnnData</option>\n+ <option value="rds_sce">RDS with a Single Cell Experiment object</option>\n+ </param>\n+ <when value="anndata">\n+ <param type="data" name="anndata_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="AnnData file" help="Select AnnData files for @VARNAME@" format="h5,h5ad"/>\n+ </when>\n+ <when value="loom">\n+ <param type="data" name="loom_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="Loom file" help="Select Loom file(s) for @VARNAME@" format="h5,h5loom"/>\n+ </when>\n+ <when value="rds_seurat">\n+ <param type="data" name="rds_seurat_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="RDS file" help="Select RDS file(s) with Seurat object for @VARNAME@" format="rdata"/>\n+ </when>\n+ <when value="rds_sce">\n+ <param type="data" name="rds_sce_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="RDS file" help="Select RDS file(s) with Single Cell Experiment object for @VARNAME@" format="rdata"/>\n+ </when>\n+ <when value="h5seurat">\n+ <param type="data" name="h5seurat_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="Seurat HDF5" help="Select Seurat HDF5 file(s) for @VARNAME" format="h5"/>\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <token name="@INPUT_OBJ_PREAMBLE@">\n+ #if $input.format == \'loom\'\n+ ln -s \'$input.loom_file\' input.loom;\n+ #else if $input.format == \'h5seurat\'\n+ ln -s \'$input.h5seurat_file\' input.h5seurat;\n+ #else if $input.format == \'anndata\'\n+ ## it complains when using links for AnnData...\n+ cp \'$input.anndata_file\' input.h5ad;\n+ #end if\n+ </token>\n+\n+ <token name="@INPUT_OBJECT@">\n+ #if $input.format == "anndata"\n+ --input-object-file input.h5ad --input-format anndata\n+ #else if $input.format == "loom"\n+ --input-object-file input.loom --input-format loom\n+ #else if $input.format == "rds_seurat"\n+ --input-object-file \'$input.rds_seurat_file\' --input-format seurat\n+ #else if $input.format == "rds_sce"\n+ --input-object-file \'$input.rds_sce_file\' --input-format singlecellexperiment\n+ #else if $input.format == "h5seurat"\n+ --input-object-file input.h5seurat --input-format h5seurat\n+ #end if\n+ </token>\n+\n+ <token name="@QUERY_OBJ_PREAMBLE@">\n+ #if $query.format == \'loom\'\n+ ln -s \'$query.loom_file\' query.loom;\n+ #else if $query.format == \'h5seurat\'\n+ ln -s \'$query.h5seurat_file\' query.h5seurat;\n+ #else if $query.format == \'anndata\'\n+ ## it complains when using links for AnnData...\n+ cp \'$query.anndata_file\' query.h5ad;\n+ #end if\n+ </token>\n+\n+ <token name="@QUERY_OBJECT@">\n+ #if $query.format == "anndata"\n+ --query-object-file query.h5ad --query-format anndata\n+ #else if $query.f'..b'e="@OUTPUT_OBJECT@">\n+ #if $format == "anndata"\n+ --output-object-file \'$anndata_file\' --output-format anndata\n+ #else if $format == "loom"\n+ --output-object-file seurat_obj.loom --output-format loom\n+ #else if $format == "rds_seurat"\n+ --output-object-file \'$rds_seurat_file\' --output-format seurat\n+ #else if $format == "rds_sce"\n+ --output-object-file \'$rds_sce_file\' --output-format singlecellexperiment\n+ #end if\n+ </token>\n+\n+ <xml name="plot_output_files_format" token_format="png">\n+ <data label="Seurat ${plot_type.plot_type_selector} on ${on_string}: @FORMAT@ plot" name="plot_out_@FORMAT@" format=\'@FORMAT@\' >\n+ <filter>plot_format == \'@FORMAT@\'</filter>\n+ </data>\n+ </xml>\n+\n+ <token name="@OUTPUT_PLOT@">\n+ #if $plot_format == "png"\n+ --plot-out \'$plot_out_png\'\n+ #else if $plot_format == "pdf"\n+ --plot-out \'$plot_out_pdf\'\n+ #else if $plot_format == "eps"\n+ --plot-out \'$plot_out_eps\'\n+ #else if $plot_format == "ps"\n+ --plot-out \'$plot_out_ps\'\n+ #else if $plot_format == "jpg"\n+ --plot-out \'$plot_out_jpg\'\n+ #else if $plot_format == "tiff"\n+ --plot-out \'$plot_out_tiff\'\n+ #else if $plot_format == "svg"\n+ --plot-out \'$plot_out_svg\'\n+ #end if\n+ </token>\n+\n+ <xml name="genes-use-input">\n+ <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv,txt,tabular" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/>\n+ </xml>\n+ <xml name="dims-use-input">\n+ <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/>\n+ </xml>\n+\n+ <token name="@SEURAT_INTRO@"><![CDATA[\n+Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.\n+It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and\n+interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse\n+types of single cell data.\n+ ]]></token>\n+\n+ <token name="@VERSION_HISTORY@"><![CDATA[\n+**Version history**\n+4.0.0: Moves to Seurat 4.0.0, introducing a number of methods for merging datasets, plus the whole suite of Seurat plots. Pablo Moreno with funding from AstraZeneca.\n+\n+3.2.3+galaxy0: Moves to Seurat 3.2.3 and introduce convert method, improving format interconversion support.\n+\n+3.1.2_0.0.8: Update metadata parsing\n+\n+3.1.1_0.0.7: Exposes perplexity and enables tab input.\n+\n+3.1.1_0.0.6+galaxy0: Moved to Seurat 3.\n+\n+ Find clusters: removed dims-use, k-param, prune-snn.\n+\n+2.3.1+galaxy0: Improved documentation and further exposition of all script\'s options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at\n+EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski (GitHub drosofff) and Lea Bellenger (GitHub bellenger-l).\n+\n+0.0.1: Initial contribution. Maria Doyle (GitHub mblue9).\n+ ]]></token>\n+\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1038/s41592-021-01102-w</citation>\n+ <citation type="doi">10.1038/nbt.4096</citation>\n+ <citation type="bibtex">\n+ @misc{r-seurat-scripts.git,\n+ author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team},\n+ year = {2018},\n+ title = {Seurat-scripts: command line interface for Seurat},\n+ publisher = {GitHub},\n+ journal = {GitHub repository},\n+ url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},\n+ }\n+ </citation>\n+ </citations>\n+ </xml>\n+</macros>\n' |
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| diff -r 000000000000 -r 95d79f1134f0 seurat_plot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seurat_plot.xml Sat Mar 02 10:40:08 2024 +0000 |
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| b'@@ -0,0 +1,726 @@\n+<tool id="seurat_plot" name="Plot" profile="18.01" version="@SEURAT_VERSION@+galaxy0">\n+ <description>with Seurat</description>\n+ <macros>\n+ <import>seurat_macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="version" />\n+ <command detect_errors="exit_code"><![CDATA[\n+ @INPUT_OBJ_PREAMBLE@\n+ seurat-plot.R\n+ @INPUT_OBJECT@\n+ @OUTPUT_PLOT@\n+ --plot-type \'$plot_type.plot_type_selector\'\n+\n+\n+ #if str($plot_type.plot_type_selector) == \'DimPlot\':\n+\n+ #if $plot_type.dims\n+ --dims \'$plot_type.dims\'\n+ #end if\n+\n+\n+ #if $plot_type.cells\n+ --cells \'$plot_type.cells\'\n+ #end if\n+\n+\n+ #if $plot_type.cols\n+ --cols \'$plot_type.cols\'\n+ #end if\n+\n+\n+ #if $plot_type.pt_size\n+ --pt-size \'$plot_type.pt_size\'\n+ #end if\n+\n+\n+ #if $plot_type.reduction\n+ --reduction \'$plot_type.reduction\'\n+ #end if\n+\n+\n+ #if $plot_type.group_by\n+ --group-by \'$plot_type.group_by\'\n+ #end if\n+\n+\n+ #if $plot_type.split_by\n+ --split-by \'$plot_type.split_by\'\n+ #end if\n+\n+\n+ #if $plot_type.shape_by\n+ --shape-by \'$plot_type.shape_by\'\n+ #end if\n+\n+\n+ #if $plot_type.order\n+ --order \'$plot_type.order\'\n+ #end if\n+\n+ $plot_type.shuffle\n+\n+\n+ --seed \'$plot_type.seed\'\n+\n+ $plot_type.label\n+\n+\n+ --label-size \'$plot_type.label_size\'\n+\n+\n+ --label-color \'$plot_type.label_color\'\n+\n+ $plot_type.label_box\n+\n+ $plot_type.repel\n+\n+\n+ #if $plot_type.cells_highlight\n+ --cells-highlight \'$plot_type.cells_highlight\'\n+ #end if\n+\n+\n+ #if $plot_type.cols_highlight\n+ --cols-highlight \'$plot_type.cols_highlight\'\n+ #end if\n+\n+\n+ #if $plot_type.sizes_highlight\n+ --sizes-highlight \'$plot_type.sizes_highlight\'\n+ #end if\n+\n+\n+ #if $plot_type.na_value\n+ --na-value \'$plot_type.na_value\'\n+ #end if\n+\n+\n+ #if $plot_type.ncol\n+ --ncol \'$plot_type.ncol\'\n+ #end if\n+\n+ #elif str($plot_type.plot_type_selector) == \'DoHeatmap\':\n+\n+ #if $plot_type.features\n+ --features \'$plot_type.features\'\n+ #end if\n+\n+\n+ #if $plot_type.cells\n+ --cells \'$plot_type.cells\'\n+ #end if\n+\n+\n+ #if $plot_type.group_by\n+ --group-by \'$plot_type.group_by\'\n+ #end if\n+\n+ $plot_type.group_bar\n+\n+\n+ #if $plot_type.group_colors\n+ --group-colors \'$plot_type.group_colors\'\n+ #end if\n+\n+\n+ #if $plot_type.disp_min\n+ --disp-min \'$plot_type.disp_min\'\n+ #end if\n+\n+\n+ #if $plot_type.disp_max\n+ --disp-max \'$plot_type.disp_max\'\n+ #end if\n+\n+\n+ --slot \'$plot_type.slot\'\n+\n+\n+ #if $plot_type.assay\n+ --assay \'$plot_type.assay\'\n+ #end if\n+\n+ $plot_type.label\n+\n+\n+ #if $plot_type.size\n+ --size \'$plot_type.size\'\n+ #end if\n+\n+\n+ #if $plot_type.hjust\n+ --hjust \'$plot_type.hjust\'\n+ #end if\n+\n+\n+ #if $plot_type.angle\n+ --angle \'$plot_type.angle\'\n+ #end if\n+\n+ $plot_type.raster\n+\n+ $plot_type.draw_lines\n+\n+\n+ #if $plot_type.lines_width\n+ --lines-width \'$plot_type.lines_width\'\n+ #end if\n+\n+\n+ #if $plot_type.group_bar_height\n+ --group-bar-height \'$plot_type.group_bar_height\'\n+ #end if\n+\n+ $plot_type.combine\n+\n+ #elif str($plot_type.plot_type_selector) == \'RidgePlot\':\n+\n+ --features \'$plot_type.features\'\n+\n+\n+ #if $plot_type.cols_ridgeplot\n+ --cols-ridgeplot \'$plot_type.cols_ridgeplot\'\n+ #end if\n+\n+\n+ #if $plot_type.idents\n+ --idents \'$plot_type.idents\'\n+ #end if\n+\n+ $plot_type.sort\n+\n+\n+ #if $plot_type.assay\n+ --assay \'$plot_type.assay\'\n+ #end if\n+\n+\n+ #if $plot_type.group_by\n+ --group-by \'$plot_type.group_by\'\n+ #end if\n+\n+ $plot_type.same_y_lims\n+\n+ $plot_type.log\n+\n+\n+ #if $plot_type.ncol\n+ --ncol \'$plot_type.ncol\'\n+ #end if\n+\n+\n+ #if $plot_type.slot\n+ --slot \'$plot_type.slot\'\n+ #end if\n+\n+ $plot_type.stack\n+\n+\n+ #if $plot_type.fill_by\n+ --fill-by \'$plot_type.fill_by\'\n+ #end if\n'..b'he plot.background fill value from the plot theme."/>\n+ <param label="Enable_output_rds_file" optional=\'true\' value=\'false\' name="enable_output_rds_file" argument="--enable_output_rds_file" type="boolean" truevalue=\'--enable_output_rds_file\' falsevalue=\'\' checked=\'false\' help="Enable output output_rds_file"/>\n+\n+ </inputs>\n+ <outputs>\n+ <expand macro="plot_output_files_format" format="png" />\n+ <expand macro="plot_output_files_format" format="pdf" />\n+ <expand macro="plot_output_files_format" format="eps" />\n+ <expand macro="plot_output_files_format" format="jpg" />\n+ <expand macro="plot_output_files_format" format="ps" />\n+ <expand macro="plot_output_files_format" format="tiff" />\n+ <expand macro="plot_output_files_format" format="svg" />\n+\n+ <data label="${tool.name} on ${on_string}: Output-rds-file" name="output_rds_file" format=\'?\'>\n+ <filter>enable_output_rds_file</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <!-- MANUAL TESTS -->\n+ <test>\n+ <param name="rds_seurat_file" ftype="rdata" value="UMAP_result_integrated.rds"/>\n+ <param name="plot_type_selector" value="FeaturePlot"/>\n+ <param name="features" value="GPC5-AS1,MAFB,FAP,PPY"/>\n+ <output name="plot_out_png" ftype="png" >\n+ <assert_contents>\n+ <has_size value="195414" delta="32000"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="rds_seurat_file" ftype="rdata" value="UMAP_result_integrated.rds"/>\n+ <param name="plot_type_selector" value="VlnPlot"/>\n+ <param name="features" value="GPC5-AS1,MAFB,FAP,PPY"/>\n+ <param name="plot_format" value="pdf"/>\n+ <output name="plot_out_pdf" ftype="pdf" >\n+ <assert_contents>\n+ <has_size value="1239200" delta="123000"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="rds_seurat_file" ftype="rdata" value="UMAP_result_integrated.rds"/>\n+ <param name="plot_type_selector" value="RidgePlot"/>\n+ <param name="features" value="GPC5-AS1,MAFB,FAP,PPY"/>\n+ <param name="plot_format" value="eps"/>\n+ <output name="plot_out_eps" ftype="eps" >\n+ <assert_contents>\n+ <has_size value="84892" delta="8400"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="rds_seurat_file" ftype="rdata" value="UMAP_result_integrated.rds"/>\n+ <param name="plot_type_selector" value="DotPlot"/>\n+ <param name="features" value="GPC5-AS1,MAFB,FAP,PPY"/>\n+ <param name="plot_format" value="ps"/>\n+ <output name="plot_out_ps" ftype="ps" >\n+ <assert_contents>\n+ <has_size value="16615" delta="1600"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="rds_seurat_file" ftype="rdata" value="UMAP_result_integrated.rds"/>\n+ <param name="plot_type_selector" value="DoHeatmap"/>\n+ <param name="features" value="GPC5-AS1,MAFB,FAP,PPY"/>\n+ <output name="plot_out_png" ftype="png" >\n+ <assert_contents>\n+ <has_size value="83227" delta="8600"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- END MANUAL TESTS -->\n+ </tests>\n+<help>\n+<!-- MANUAL HELP -->\n+<![CDATA[\n+.. class:: infomark\n+\n+**What it does**\n+\n+@SEURAT_INTRO@\n+\n+This tool produces the different plots available on Seurat.\n+\n+-----\n+\n+**Inputs**\n+\n+* Seurat object or compatible (can be specified in different formats)\n+* Plot type (can be specified in different formats)\n+* Potential compulsory options for each plot type\n+\n+All the rest of the parameters are optional.\n+\n+-----\n+\n+**Outputs**\n+\n+* A plot in the specified format\n+* Optionally, an RDS object with the ggplo2 plot.\n+\n+@VERSION_HISTORY@\n+\n+]]>\n+<!-- END MANUAL HELP -->\n+</help>\n+ <expand macro="citations" />\n+</tool>\n' |