Mercurial > repos > iuc > goseq
changeset 11:602de62d995b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c
| author | iuc |
|---|---|
| date | Wed, 11 Jan 2023 10:13:15 +0000 |
| parents | 43798b4caee0 |
| children | |
| files | goseq.r goseq.xml test-data/dge_list.tab test-data/goseq_analysis.RData test-data/nobias.tab |
| diffstat | 5 files changed, 25 insertions(+), 825 deletions(-) [+] |
line wrap: on
line diff
--- 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]),
--- 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 @@ -<tool id="goseq" name="goseq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> +<tool id="goseq" name="goseq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01"> <description>tests for overrepresented gene categories</description> - <xrefs> - <xref type="bio.tools">goseq</xref> - </xrefs> + <macros> + <token name="@TOOL_VERSION@">1.50.0</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> <edam_topics> <edam_topic>topic_3308</edam_topic> </edam_topics> <edam_operations> <edam_operation>operation_2436</edam_operation> </edam_operations> - <macros> - <token name="@TOOL_VERSION@">1.44.0</token> - <token name="@VERSION_SUFFIX@">2</token> - </macros> + <xrefs> + <xref type="bio.tools">goseq</xref> + </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">bioconductor-goseq</requirement> - <requirement type="package" version="3.13.0">bioconductor-org.hs.eg.db</requirement> - <requirement type="package" version="3.13.0">bioconductor-org.dm.eg.db</requirement> - <requirement type="package" version="3.13.0">bioconductor-org.dr.eg.db</requirement> - <requirement type="package" version="3.13.0">bioconductor-org.mm.eg.db</requirement> - <requirement type="package" version="3.13.0">bioconductor-org.rn.eg.db</requirement> - <requirement type="package" version="1.0.9">r-dplyr</requirement> - <requirement type="package" version="3.3.6">r-ggplot2</requirement> - <requirement type="package" version="1.7.1">r-optparse</requirement> - <requirement type="package" version="1.1.1o">openssl</requirement> + <requirement type="package" version="3.16.0">bioconductor-org.hs.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.dr.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="1.0.10">r-dplyr</requirement> + <requirement type="package" version="3.4.0">r-ggplot2</requirement> + <requirement type="package" version="1.7.3">r-optparse</requirement> + <requirement type="package" version="1.1.1s">openssl</requirement> </requirements> <stdio> <regex match="Execution halted" @@ -239,7 +239,7 @@ <output name="wallenius_tab"> <assert_contents> <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" /> - <has_text_matching expression="GO:0005576.*0.9" /> + <has_text_matching expression="GO:0012501.*0.01"/> </assert_contents> </output> <output name="cat_genes_tab"> @@ -277,7 +277,7 @@ <output name="wallenius_tab"> <assert_contents> <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" /> - <has_text_matching expression="GO:0016569.*0.90" /> + <has_text_matching expression="GO:0015748.*0.02" /> </assert_contents> </output> </test> @@ -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:
--- 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 -ENSG00000165983 True -ENSG00000238221 False -ENSG00000184831 False 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--- 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