| Previous changeset 25:d6f5fa4ee473 (2022-03-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738 |
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modified:
limma_voom.R limma_voom.xml |
| b |
| diff -r d6f5fa4ee473 -r 119b069fc845 limma_voom.R --- a/limma_voom.R Tue Mar 01 08:03:53 2022 +0000 +++ b/limma_voom.R Fri Feb 09 17:06:25 2024 +0000 |
| [ |
| b'@@ -46,7 +46,21 @@\n # Modified by: Maria Doyle - Jun 2017, Jan 2018, May 2018\n \n # Record starting time\n-time_start <- as.character(Sys.time())\n+time_start <- Sys.time()\n+\n+# Setup R error handling to go to stderr\n+options(\n+ show.error.messages = FALSE,\n+ error = function() {\n+ cat(geterrmessage(), file = stderr())\n+ q("no", 1, FALSE)\n+ }\n+)\n+\n+# Unify locale settings\n+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")\n+\n+warnings()\n \n # Load all required libraries\n library(methods, quietly = TRUE, warn.conflicts = FALSE)\n@@ -106,19 +120,19 @@\n # Create cata function: default path set, default seperator empty and appending\n # true by default (Ripped straight from the cat function with altered argument\n # defaults)\n-cata <- function(..., file = opt$htmlPath, sep = "", fill = FALSE, labels = NULL,\n- append = TRUE) {\n- if (is.character(file))\n- if (file == "")\n+cata <- function(..., file = opt$htmlPath, sep = "", fill = FALSE,\n+ labels = NULL, append = TRUE) {\n+ if (is.character(file)) {\n+ if (file == "") {\n file <- stdout()\n- else if (substring(file, 1L, 1L) == "|") {\n+ } else if (substring(file, 1L, 1L) == "|") {\n file <- pipe(substring(file, 2L), "w")\n on.exit(close(file))\n+ } else {\n+ file <- file(file, ifelse(append, "a", "w"))\n+ on.exit(close(file))\n }\n- else {\n- file <- file(file, ifelse(append, "a", "w"))\n- on.exit(close(file))\n- }\n+ }\n .Internal(cat(list(...), file, sep, fill, labels, append))\n }\n \n@@ -162,39 +176,42 @@\n \n # Get options, using the spec as defined by the enclosed list.\n # Read the options from the default: commandArgs(TRUE).\n-spec <- matrix(c(\n- "htmlPath", "R", 1, "character",\n- "outPath", "o", 1, "character",\n- "filesPath", "j", 2, "character",\n- "matrixPath", "m", 2, "character",\n- "factFile", "f", 2, "character",\n- "factInput", "i", 2, "character",\n- "annoPath", "a", 2, "character",\n- "contrastFile", "C", 1, "character",\n- "contrastInput", "D", 1, "character",\n- "cpmReq", "c", 1, "double",\n- "totReq", "y", 0, "logical",\n- "cntReq", "z", 1, "integer",\n- "sampleReq", "s", 1, "integer",\n- "filtCounts", "F", 0, "logical",\n- "normCounts", "x", 0, "logical",\n- "rdaOpt", "r", 0, "logical",\n- "lfcReq", "l", 1, "double",\n- "pValReq", "p", 1, "double",\n- "pAdjOpt", "d", 1, "character",\n- "normOpt", "n", 1, "character",\n- "robOpt", "b", 0, "logical",\n- "trend", "t", 1, "double",\n- "weightOpt", "w", 0, "logical",\n- "topgenes", "G", 1, "integer",\n- "treatOpt", "T", 0, "logical",\n- "plots", "P", 1, "character",\n- "libinfoOpt", "L", 0, "logical"),\n- byrow = TRUE, ncol = 4)\n+spec <- matrix(\n+ c(\n+ "htmlPath", "R", 1, "character",\n+ "outPath", "o", 1, "character",\n+ "filesPath", "j", 2, "character",\n+ "matrixPath", "m", 2, "character",\n+ "factFile", "f", 2, "character",\n+ "factInput", "i", 2, "character",\n+ "annoPath", "a", 2, "character",\n+ "contrastFile", "C", 1, "character",\n+ "contrastInput", "D", 1, "character",\n+ "cpmReq", "c", 1, "double",\n+ "totReq", "y", 0, "logical",\n+ "cntReq", "z", 1, "integer",\n+ "sampleReq", "s", 1, "integer",\n+ "filtCounts", "F", 0, "logical",\n+ "normCounts", "x", 0, "logical",\n+ "rdaOpt", "r", 0, "logical",\n+ "lfcReq", "l", 1, "double",\n+ "pValReq", "p", 1, "double",\n+ "pAdjOpt", "d", 1, "character",\n+ "normOpt", "n", 1, "character",\n+ "robOpt", "b", 0, "logical",\n+ "trend", "t", 1, "double",\n+ "weightOpt", "w", 0, "logical",\n+ "topgenes", "G", 1, "integer",\n+ "treatOpt", "T", 0, "logical",\n+ "plots", "P", 1, "character",\n+ "libinfoOpt", "L", 0, "logical"\n+ ),\n+ byrow = TRUE, ncol = 4\n+)\n opt <- getopt(spec)\n \n \n-if ('..b'ste("Robinson MD and Smyth GK (2008). Small-sample estimation of",\n- "negative binomial dispersion, with applications to SAGE data.",\n- "Biostatistics, 9, 321-332")\n-cit[9] <- paste("McCarthy DJ, Chen Y and Smyth GK (2012). Differential",\n- "expression analysis of multifactor RNA-Seq experiments with",\n- "respect to biological variation. Nucleic Acids Research 40,",\n- "4288-4297")\n-cit[10] <- paste("Law CW, Chen Y, Shi W, and Smyth GK (2014). Voom:",\n- "precision weights unlock linear model analysis tools for",\n- "RNA-seq read counts. Genome Biology 15, R29.")\n-cit[11] <- paste("Ritchie ME, Diyagama D, Neilson J, van Laar R,",\n- "Dobrovic A, Holloway A and Smyth GK (2006).",\n- "Empirical array quality weights for microarray data.",\n- "BMC Bioinformatics 7, Article 261.")\n+cit[2] <- paste(\n+ "Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, Blewitt ME,",\n+ "Asselin-Labat ML, Smyth GK, Ritchie ME (2015). Why weight? ",\n+ "Modelling sample and observational level variability improves power ",\n+ "in RNA-seq analyses. Nucleic Acids Research, 43(15), e97."\n+)\n+cit[3] <- paste(\n+ "Please cite the paper below for the limma software itself.",\n+ "Please also try to cite the appropriate methodology articles",\n+ "that describe the statistical methods implemented in limma,",\n+ "depending on which limma functions you are using. The",\n+ "methodology articles are listed in Section 2.1 of the",\n+ link[1],\n+ "Cite no. 3 only if sample weights were used."\n+)\n+cit[4] <- paste(\n+ "Smyth GK (2005). Limma: linear models for microarray data.",\n+ "In: \'Bioinformatics and Computational Biology Solutions using",\n+ "R and Bioconductor\'. R. Gentleman, V. Carey, S. doit,.",\n+ "Irizarry, W. Huber (eds), Springer, New York, pages 397-420."\n+)\n+cit[5] <- paste(\n+ "Please cite the first paper for the software itself and the",\n+ "other papers for the various original statistical methods",\n+ "implemented in edgeR. See Section 1.2 in the", link[2],\n+ "for more detail."\n+)\n+cit[6] <- paste(\n+ "Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a",\n+ "Bioconductor package for differential expression analysis",\n+ "of digital gene expression data. Bioinformatics 26, 139-140"\n+)\n+cit[7] <- paste(\n+ "Robinson MD and Smyth GK (2007). Moderated statistical tests",\n+ "for assessing differences in tag abundance. Bioinformatics",\n+ "23, 2881-2887"\n+)\n+cit[8] <- paste(\n+ "Robinson MD and Smyth GK (2008). Small-sample estimation of",\n+ "negative binomial dispersion, with applications to SAGE data.",\n+ "Biostatistics, 9, 321-332"\n+)\n+cit[9] <- paste(\n+ "McCarthy DJ, Chen Y and Smyth GK (2012). Differential",\n+ "expression analysis of multifactor RNA-Seq experiments with",\n+ "respect to biological variation. Nucleic Acids Research 40,",\n+ "4288-4297"\n+)\n+cit[10] <- paste(\n+ "Law CW, Chen Y, Shi W, and Smyth GK (2014). Voom:",\n+ "precision weights unlock linear model analysis tools for",\n+ "RNA-seq read counts. Genome Biology 15, R29."\n+)\n+cit[11] <- paste(\n+ "Ritchie ME, Diyagama D, Neilson J, van Laar R,",\n+ "Dobrovic A, Holloway A and Smyth GK (2006).",\n+ "Empirical array quality weights for microarray data.",\n+ "BMC Bioinformatics 7, Article 261."\n+)\n cata("<h3>Citations</h3>\\n")\n cata(cit[1], "\\n")\n cata("<br>\\n")\n@@ -1338,13 +1423,16 @@\n \n cata("<table border=\\"0\\">\\n")\n cata("<tr>\\n")\n-table_item("Task started at:"); table_item(time_start)\n+table_item("Task started at:")\n+table_item(time_start)\n cata("</tr>\\n")\n cata("<tr>\\n")\n-table_item("Task ended at:"); table_item(time_end)\n+table_item("Task ended at:")\n+table_item(time_end)\n cata("</tr>\\n")\n cata("<tr>\\n")\n-table_item("Task run time:"); table_item(time_taken)\n+table_item("Task run time:")\n+table_item(time_taken)\n cata("<tr>\\n")\n cata("</table>\\n")\n \n' |
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| diff -r d6f5fa4ee473 -r 119b069fc845 limma_voom.xml --- a/limma_voom.xml Tue Mar 01 08:03:53 2022 +0000 +++ b/limma_voom.xml Fri Feb 09 17:06:25 2024 +0000 |
| [ |
| @@ -1,13 +1,12 @@ -<tool id="limma_voom" name="limma" version="@TOOL_VERSION@+galaxy0"> +<tool id="limma_voom" name="limma" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description> Perform differential expression with limma-voom or limma-trend </description> <macros> - <token name="@TOOL_VERSION@">3.50.1</token> + <token name="@TOOL_VERSION@">3.58.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.0</token> </macros> - <xrefs> - <xref type="bio.tools">limma</xref> - </xrefs> <edam_topics> <edam_topic>topic_3308</edam_topic> </edam_topics> @@ -15,16 +14,20 @@ <edam_operation>operation_3563</edam_operation> <edam_operation>operation_3223</edam_operation> </edam_operations> + <xrefs> + <xref type="bio.tools">limma</xref> + <xref type="bioconductor">limma</xref> + </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">bioconductor-limma</requirement> - <requirement type="package" version="3.36.0">bioconductor-edger</requirement> - <requirement type="package" version="1.4.36">r-statmod</requirement> - <requirement type="package" version="1.1.1">r-scales</requirement> + <requirement type="package" version="4.0.2">bioconductor-edger</requirement> + <requirement type="package" version="1.5.0">r-statmod</requirement> + <requirement type="package" version="1.3.0">r-scales</requirement> <requirement type="package" version="0.2.21">r-rjson</requirement> - <requirement type="package" version="1.20.3">r-getopt</requirement> - <requirement type="package" version="3.1.1">r-gplots</requirement> - <requirement type="package" version="2.4.0">bioconductor-glimma</requirement> + <requirement type="package" version="1.20.4">r-getopt</requirement> + <requirement type="package" version="3.1.3.1">r-gplots</requirement> + <requirement type="package" version="2.12.0">bioconductor-glimma</requirement> </requirements> <version_command><![CDATA[ @@ -733,6 +736,12 @@ <param name="normalisationOption" value="TMM" /> <param name="topgenes" value="6" /> <output_collection name="outTables" count="3"> + <element name="limma-voom_Mut-WT-WT-Mut" ftype="tabular" > + <assert_contents> + <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> + <has_text_matching expression="11304.*0.9146" /> + </assert_contents> + </element> <element name="limma-voom_Mut-WT" ftype="tabular" > <assert_contents> <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> @@ -745,12 +754,6 @@ <has_text_matching expression="11304.*-0.4573" /> </assert_contents> </element> - <element name="limma-voom_Mut-WT-WT-Mut" ftype="tabular" > - <assert_contents> - <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> - <has_text_matching expression="11304.*0.9146" /> - </assert_contents> - </element> </output_collection> </test> </tests> |