# HG changeset patch # User iuc # Date 1673431995 0 # Node ID 602de62d995b61c68cf5e9fc2c931baff2bee33e # Parent 43798b4caee0a1ad35dfb28ca5dcd4f92626d183 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c diff -r 43798b4caee0 -r 602de62d995b goseq.r --- a/goseq.r Thu Jun 09 13:01:48 2022 +0000 +++ b/goseq.r Wed Jan 11 10:13:15 2023 +0000 @@ -1,6 +1,6 @@ -options(show.error.messages = F, error = function() { +options(show.error.messages = FALSE, error = function() { cat(geterrmessage(), file = stderr()) - q("no", 1, F) + q("no", 1, FALSE) }) # we need that to not crash galaxy with an UTF8 error on German LC settings. @@ -146,7 +146,7 @@ ) # Compare sampling with wallenius - if (args$make_plots & !is.null(args$wallenius_tab)) { + if (args$make_plots && !is.null(args$wallenius_tab)) { pdf(args$sample_vs_wallenius_plot) plot(log10(results[["Wallenius"]][, 2]), log10(results[["Sampling"]][match(results[["Sampling"]][, 1], results[["Wallenius"]][, 1]), 2]), diff -r 43798b4caee0 -r 602de62d995b goseq.xml --- a/goseq.xml Thu Jun 09 13:01:48 2022 +0000 +++ b/goseq.xml Wed Jan 11 10:13:15 2023 +0000 @@ -1,29 +1,29 @@ - + tests for overrepresented gene categories - - goseq - + + 1.50.0 + 0 + topic_3308 operation_2436 - - 1.44.0 - 2 - + + goseq + bioconductor-goseq - bioconductor-org.hs.eg.db - bioconductor-org.dm.eg.db - bioconductor-org.dr.eg.db - bioconductor-org.mm.eg.db - bioconductor-org.rn.eg.db - r-dplyr - r-ggplot2 - r-optparse - openssl + bioconductor-org.hs.eg.db + bioconductor-org.dm.eg.db + bioconductor-org.dr.eg.db + bioconductor-org.mm.eg.db + bioconductor-org.rn.eg.db + r-dplyr + r-ggplot2 + r-optparse + openssl - + @@ -277,7 +277,7 @@ - + @@ -401,7 +401,7 @@ *Differentially expressed genes file* -goseq needs a tabular file containing information on differentially expressed genes. This should contain all genes assayed in the RNA-seq experiment. The file should have two columns with an optional header row. The first column should contain the Gene IDs, which must be unique within the file and not repeated. The second column should contain True or False. True means the gene should count as differentially expressed, False means it is not differentially expressed. You can use the "Compute an expression on every row" tool to create a True / False column for your dataset. +goseq needs a tabular file containing information on differentially expressed genes. This should contain all genes assayed in the RNA-seq experiment. The file should have two columns with an optional header row. The first column should contain the Gene IDs, which must be unique within the file and not repeated. The second column should contain True or False. True means the gene should count as differentially expressed, False means it is not differentially expressed. You can use the "Compute on rows" tool to create a True / False column for your dataset. Example: diff -r 43798b4caee0 -r 602de62d995b test-data/dge_list.tab --- a/test-data/dge_list.tab Thu Jun 09 13:01:48 2022 +0000 +++ b/test-data/dge_list.tab Wed Jan 11 10:13:15 2023 +0000 @@ -198,803 +198,3 @@ ENSG00000165905 False ENSG00000072958 False ENSG00000113048 True -ENSG00000237017 False -ENSG00000186583 False -ENSG00000235623 False -ENSG00000124120 False -ENSG00000100027 False -ENSG00000173674 False -ENSG00000226067 False -ENSG00000243122 False -ENSG00000111707 False -ENSG00000230022 False -ENSG00000143337 False -ENSG00000172086 False -ENSG00000173153 False -ENSG00000138594 False -ENSG00000225806 False -ENSG00000197961 False -ENSG00000161277 False -ENSG00000107833 True -ENSG00000236681 False -ENSG00000147684 False -ENSG00000230118 False -ENSG00000173366 False -ENSG00000100106 False -ENSG00000236680 False -ENSG00000187605 False -ENSG00000059122 False -ENSG00000188997 False -ENSG00000165521 True -ENSG00000235065 True -ENSG00000108091 False -ENSG00000113328 False 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False -ENSG00000198482 False -ENSG00000173681 False -ENSG00000204164 False -ENSG00000228612 False -ENSG00000003096 True -ENSG00000180881 False -ENSG00000205084 False -ENSG00000159173 False -ENSG00000197535 False -ENSG00000223382 True -ENSG00000183309 False -ENSG00000215099 False -ENSG00000116685 False -ENSG00000181472 False -ENSG00000132274 False -ENSG00000145494 False -ENSG00000122644 True -ENSG00000157107 True -ENSG00000145354 False -ENSG00000158467 False -ENSG00000164934 False -ENSG00000134986 True -ENSG00000121988 False -ENSG00000178996 False diff -r 43798b4caee0 -r 602de62d995b test-data/goseq_analysis.RData Binary file test-data/goseq_analysis.RData has changed diff -r 43798b4caee0 -r 602de62d995b test-data/nobias.tab --- a/test-data/nobias.tab Thu Jun 09 13:01:48 2022 +0000 +++ b/test-data/nobias.tab Wed Jan 11 10:13:15 2023 +0000 @@ -1,3 +1,3 @@ category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology p_adjust_over_represented p_adjust_under_represented -GO:0000278 0.0129827306163772 0.999244816412166 4 5 mitotic cell cycle BP 0.0259654612327543 0.999244816412166 -GO:0000003 1 0.761 0 1 reproduction BP 1 0.999244816412166 +GO:0000278 0.0104514596186152 0.999459407261106 4 5 mitotic cell cycle BP 0.0209029192372304 0.999459407261106 +GO:0000003 1 0.77 0 1 reproduction BP 1 0.999459407261106