| Previous changeset 0:28e29a3d0eda (2023-06-07) Next changeset 2:e08383c04167 (2025-02-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 945cc63f011002e3f61d7e848d556b647e9c8878 |
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modified:
macros.xml multiGSEA.R multigsea.xml |
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| diff -r 28e29a3d0eda -r e48b10ce08b8 macros.xml --- a/macros.xml Wed Jun 07 19:48:50 2023 +0000 +++ b/macros.xml Wed Feb 21 15:41:52 2024 +0000 |
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| @@ -1,23 +1,23 @@ <macros> - <token name="@TOOL_VERSION@">1.8.0</token> + <token name="@TOOL_VERSION@">1.12.0</token> <token name="@SUFFIX_VERSION@">0</token> <token name="@PROFILE@">20.05</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bioconductor-multigsea</requirement> - <requirement type="package" version="2.2.1">r-argparse</requirement> + <requirement type="package" version="2.2.2">r-argparse</requirement> <requirement type="package" version="1.0.0">bioconductor-metaboliteidmapping</requirement> - <requirement type="package" version="3.16.0">bioconductor-org.Hs.eg.db</requirement> - <requirement type="package" version="3.16.0">bioconductor-org.Mm.eg.db</requirement> - <requirement type="package" version="3.16.0">bioconductor-org.Rn.eg.db</requirement> - <requirement type="package" version="3.16.0">bioconductor-org.Cf.eg.db</requirement> - <requirement type="package" version="3.16.0">bioconductor-org.Bt.eg.db</requirement> - <requirement type="package" version="3.16.0">bioconductor-org.Ss.eg.db</requirement> - <requirement type="package" version="3.16.0">bioconductor-org.Gg.eg.db</requirement> - <requirement type="package" version="3.16.0">bioconductor-org.Xl.eg.db</requirement> - <requirement type="package" version="3.16.0">bioconductor-org.Dr.eg.db</requirement> - <requirement type="package" version="3.16.0">bioconductor-org.Dm.eg.db</requirement> - <requirement type="package" version="3.16.0">bioconductor-org.Ce.eg.db</requirement> + <requirement type="package" version="3.18.0">bioconductor-org.Hs.eg.db</requirement> + <requirement type="package" version="3.18.0">bioconductor-org.Mm.eg.db</requirement> + <requirement type="package" version="3.18.0">bioconductor-org.Rn.eg.db</requirement> + <requirement type="package" version="3.18.0">bioconductor-org.Cf.eg.db</requirement> + <requirement type="package" version="3.18.0">bioconductor-org.Bt.eg.db</requirement> + <requirement type="package" version="3.18.0">bioconductor-org.Ss.eg.db</requirement> + <requirement type="package" version="3.18.0">bioconductor-org.Gg.eg.db</requirement> + <requirement type="package" version="3.18.0">bioconductor-org.Xl.eg.db</requirement> + <requirement type="package" version="3.18.0">bioconductor-org.Dr.eg.db</requirement> + <requirement type="package" version="3.18.0">bioconductor-org.Dm.eg.db</requirement> + <requirement type="package" version="3.18.0">bioconductor-org.Ce.eg.db</requirement> </requirements> </xml> <xml name="citations"> |
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| diff -r 28e29a3d0eda -r e48b10ce08b8 multiGSEA.R --- a/multiGSEA.R Wed Jun 07 19:48:50 2023 +0000 +++ b/multiGSEA.R Wed Feb 21 15:41:52 2024 +0000 |
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| b'@@ -1,6 +1,7 @@\n library(multiGSEA,\n- quietly = TRUE,\n- warn.conflicts = FALSE)\n+ quietly = TRUE,\n+ warn.conflicts = FALSE\n+)\n library(argparse, quietly = TRUE, warn.conflicts = FALSE)\n \n ################################################################################\n@@ -11,56 +12,69 @@\n # Collect arguments from command line\n parser <- ArgumentParser(description = "multiGSEA R script")\n \n-parser$add_argument("--transcriptomics", required = FALSE,\n- help = "Transcriptomics data")\n+parser$add_argument("--transcriptomics",\n+ required = FALSE,\n+ help = "Transcriptomics data"\n+)\n parser$add_argument(\n- "--transcriptome_ids",\n- required = FALSE,\n- help = "Transcriptomics ids",\n- default = "SYMBOL"\n+ "--transcriptome_ids",\n+ required = FALSE,\n+ help = "Transcriptomics ids",\n+ default = "SYMBOL"\n )\n-parser$add_argument("--proteomics", required = FALSE,\n- help = "Proteomics data")\n+parser$add_argument("--proteomics",\n+ required = FALSE,\n+ help = "Proteomics data"\n+)\n parser$add_argument(\n- "--proteome_ids",\n- required = FALSE,\n- help = "Proteomics ids",\n- default = "SYMBOL"\n+ "--proteome_ids",\n+ required = FALSE,\n+ help = "Proteomics ids",\n+ default = "SYMBOL"\n )\n-parser$add_argument("--metabolomics", required = FALSE,\n- help = "Metabolomics data")\n+parser$add_argument("--metabolomics",\n+ required = FALSE,\n+ help = "Metabolomics data"\n+)\n parser$add_argument(\n- "--metabolome_ids",\n- required = FALSE,\n- help = "Metabolomics ids",\n- default = "HMDB"\n+ "--metabolome_ids",\n+ required = FALSE,\n+ help = "Metabolomics ids",\n+ default = "HMDB"\n )\n-parser$add_argument("--organism", required = TRUE,\n- help = "Organism")\n-parser$add_argument("--combine_pvalues", required = TRUE,\n- help = "Combine p-values method")\n-parser$add_argument("--padj_method", required = TRUE,\n- help = "P-adjustment method")\n+parser$add_argument("--organism",\n+ required = TRUE,\n+ help = "Organism"\n+)\n+parser$add_argument("--combine_pvalues",\n+ required = TRUE,\n+ help = "Combine p-values method"\n+)\n+parser$add_argument("--padj_method",\n+ required = TRUE,\n+ help = "P-adjustment method"\n+)\n parser$add_argument("--databases",\n- required = TRUE,\n- help = "Pathway databases")\n+ required = TRUE,\n+ help = "Pathway databases"\n+)\n \n args <- parser$parse_args()\n \n ## ----Load library-------------------------------------------------------------\n \n organism_mapping <- c(\n- "hsapiens" = "org.Hs.eg.db",\n- "mmusculus" = "org.Mm.eg.db",\n- "rnorvegicus" = "org.Rn.eg.db",\n- "cfamiliaris" = "org.Cf.eg.db",\n- "btaurus" = "org.Bt.eg.db",\n- "sscrofa" = "org.Ss.eg.db",\n- "ggallus" = "org.Gg.eg.db",\n- "drerio" = "org.Xl.eg.db",\n- "xlaevis" = "org.Dr.eg.db",\n- "dmelanogaster" = "org.Dm.eg.db",\n- "celegans" = "org.Ce.eg.db"\n+ "hsapiens" = "org.Hs.eg.db",\n+ "mmusculus" = "org.Mm.eg.db",\n+ "rnorvegicus" = "org.Rn.eg.db",\n+ "cfamiliaris" = "org.Cf.eg.db",\n+ "btaurus" = "org.Bt.eg.db",\n+ "sscrofa" = "org.Ss.eg.db",\n+ "ggallus" = "org.Gg.eg.db",\n+ "drerio" = "org.Xl.eg.db",\n+ "xlaevis" = "org.Dr.eg.db",\n+ "dmelanogaster" = "org.Dm.eg.db",\n+ "celegans" = "org.Ce.eg.db"\n )\n \n library(organism_mapping[args$organism], character.only = TRUE)\n@@ -71,29 +85,31 @@\n layer <- c()\n \n if (!is.null(args$transcriptomics)) {\n- transcriptome <- read.csv(\n- args$transcriptomics,\n- header = TRUE,\n- sep = "\\t",\n- dec = "."\n- )\n- layer <- append(layer, "transcriptome")\n+ transcriptome <- read.csv(\n+ args$transcriptomics,\n+ header = TRUE,\n+ sep = "\\t",\n+ dec = "."\n+ )\n+ layer <- append(layer, "transcriptome")\n }\n \n if (!is.null(args$proteomics)) {\n- proteome <- read.csv(args$proteomics,\n- header = TRUE,\n- sep = "\\t",\n- '..b'"."\n+ )\n+ layer <- append(layer, "proteome")\n }\n \n if (!is.null(args$metabolomics)) {\n- metabolome <- read.csv(args$metabolomics,\n- header = TRUE,\n- sep = "\\t",\n- dec = ".")\n- layer <- append(layer, "metabolome")\n+ metabolome <- read.csv(args$metabolomics,\n+ header = TRUE,\n+ sep = "\\t",\n+ dec = "."\n+ )\n+ layer <- append(layer, "metabolome")\n }\n \n ## ----rank_features------------------------------------------------------------\n@@ -103,70 +119,76 @@\n \n ## add transcriptome layer\n if (!is.null(args$transcriptomics)) {\n- omics_data$transcriptome <- rankFeatures(transcriptome$logFC,\n- transcriptome$pValue)\n- names(omics_data$transcriptome) <- transcriptome$Symbol\n+ omics_data$transcriptome <- rankFeatures(\n+ transcriptome$logFC,\n+ transcriptome$pValue\n+ )\n+ names(omics_data$transcriptome) <- transcriptome$Symbol\n }\n \n ## add proteome layer\n if (!is.null(args$proteomics)) {\n- omics_data$proteome <- rankFeatures(proteome$logFC, proteome$pValue)\n- names(omics_data$proteome) <- proteome$Symbol\n+ omics_data$proteome <- rankFeatures(proteome$logFC, proteome$pValue)\n+ names(omics_data$proteome) <- proteome$Symbol\n }\n \n ## add metabolome layer\n ## HMDB features have to be updated to the new HMDB format\n if (!is.null(args$metabolomics)) {\n- omics_data$metabolome <-\n- rankFeatures(metabolome$logFC, metabolome$pValue)\n- names(omics_data$metabolome) <- metabolome$HMDB\n- names(omics_data$metabolome) <- gsub("HMDB", "HMDB00",\n- names(omics_data$metabolome))\n+ omics_data$metabolome <-\n+ rankFeatures(metabolome$logFC, metabolome$pValue)\n+ names(omics_data$metabolome) <- metabolome$HMDB\n+ names(omics_data$metabolome) <- gsub(\n+ "HMDB", "HMDB00",\n+ names(omics_data$metabolome)\n+ )\n }\n \n \n ## remove NA\'s and sort feature ranks\n omics_data <- lapply(omics_data, function(vec) {\n- sort(vec[!is.na(vec)])\n+ sort(vec[!is.na(vec)])\n })\n \n ## ----Pathway definitions------------------------------------------------------\n \n pathways <-\n- getMultiOmicsFeatures(\n- dbs = unlist(strsplit(args$databases, ",", fixed = TRUE)),\n- layer = layer,\n- returnTranscriptome = args$transcriptome_ids,\n- returnProteome = args$proteome_ids,\n- returnMetabolome = args$metabolome_ids,\n- organism = args$organism,\n- useLocal = FALSE\n- )\n+ getMultiOmicsFeatures(\n+ dbs = unlist(strsplit(args$databases, ",", fixed = TRUE)),\n+ layer = layer,\n+ returnTranscriptome = args$transcriptome_ids,\n+ returnProteome = args$proteome_ids,\n+ returnMetabolome = args$metabolome_ids,\n+ organism = args$organism,\n+ useLocal = FALSE\n+ )\n \n ## ----calculate enrichment-----------------------------------------------------\n \n enrichment_scores <-\n- multiGSEA(pathways, omics_data)\n+ multiGSEA(pathways, omics_data)\n \n ## ----combine_pvalues----------------------------------------------------------\n \n-df <- extractPvalues(enrichmentScores = enrichment_scores,\n- pathwayNames = names(pathways[[1]]))\n+df <- extractPvalues(\n+ enrichmentScores = enrichment_scores,\n+ pathwayNames = names(pathways[[1]])\n+)\n \n df$combined_pval <-\n- combinePvalues(df, method = args$combine_pvalues)\n+ combinePvalues(df, method = args$combine_pvalues)\n df$combined_padj <-\n- p.adjust(df$combined_pval, method = args$padj_method)\n+ p.adjust(df$combined_pval, method = args$padj_method)\n \n df <- cbind(data.frame(pathway = names(pathways[[1]])), df)\n \n ## ----Write output-------------------------------------------------------------\n \n write.table(\n- df,\n- file = "results.tsv",\n- quote = FALSE,\n- sep = "\\t",\n- col.names = TRUE,\n- row.names = FALSE\n+ df,\n+ file = "results.tsv",\n+ quote = FALSE,\n+ sep = "\\t",\n+ col.names = TRUE,\n+ row.names = FALSE\n )\n' |
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| diff -r 28e29a3d0eda -r e48b10ce08b8 multigsea.xml --- a/multigsea.xml Wed Jun 07 19:48:50 2023 +0000 +++ b/multigsea.xml Wed Feb 21 15:41:52 2024 +0000 |
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| @@ -144,6 +144,8 @@ <output name="output"> <assert_contents> <has_size value="43574" delta="300"/> + <has_n_lines n="327"/> + <has_n_columns n="9"/> <has_text text="Ubiquinone and other terpenoid-quinone biosynthesis"/> </assert_contents> </output> @@ -171,7 +173,8 @@ </conditional> <output name="output"> <assert_contents> - <has_size value="42541" delta="300"/> + <has_n_lines n="327"/> + <has_n_columns n="9"/> <has_text text="Ubiquinone and other terpenoid-quinone biosynthesis"/> </assert_contents> </output> |