| Previous changeset 20:0921444c832d (2019-05-29) Next changeset 22:708348a17fa1 (2021-06-26) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5" |
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modified:
limma_voom.R limma_voom.xml |
| b |
| diff -r 0921444c832d -r 58c35179ebf0 limma_voom.R --- a/limma_voom.R Wed May 29 10:31:41 2019 -0400 +++ b/limma_voom.R Fri Jun 04 20:37:04 2021 +0000 |
| [ |
| b'@@ -46,24 +46,24 @@\n # Modified by: Maria Doyle - Jun 2017, Jan 2018, May 2018\n \n # Record starting time\n-timeStart <- as.character(Sys.time())\n+time_start <- as.character(Sys.time())\n \n # Load all required libraries\n-library(methods, quietly=TRUE, warn.conflicts=FALSE)\n-library(statmod, quietly=TRUE, warn.conflicts=FALSE)\n-library(splines, quietly=TRUE, warn.conflicts=FALSE)\n-library(edgeR, quietly=TRUE, warn.conflicts=FALSE)\n-library(limma, quietly=TRUE, warn.conflicts=FALSE)\n-library(scales, quietly=TRUE, warn.conflicts=FALSE)\n-library(getopt, quietly=TRUE, warn.conflicts=FALSE)\n-library(gplots, quietly=TRUE, warn.conflicts=FALSE)\n+library(methods, quietly = TRUE, warn.conflicts = FALSE)\n+library(statmod, quietly = TRUE, warn.conflicts = FALSE)\n+library(splines, quietly = TRUE, warn.conflicts = FALSE)\n+library(edgeR, quietly = TRUE, warn.conflicts = FALSE)\n+library(limma, quietly = TRUE, warn.conflicts = FALSE)\n+library(scales, quietly = TRUE, warn.conflicts = FALSE)\n+library(getopt, quietly = TRUE, warn.conflicts = FALSE)\n+library(gplots, quietly = TRUE, warn.conflicts = FALSE)\n \n ################################################################################\n ### Function Declaration\n ################################################################################\n # Function to sanitise contrast equations so there are no whitespaces\n # surrounding the arithmetic operators, leading or trailing whitespace\n-sanitiseEquation <- function(equation) {\n+sanitise_equation <- function(equation) {\n equation <- gsub(" *[+] *", "+", equation)\n equation <- gsub(" *[-] *", "-", equation)\n equation <- gsub(" *[/] *", "/", equation)\n@@ -73,33 +73,33 @@\n }\n \n # Function to sanitise group information\n-sanitiseGroups <- function(string) {\n+sanitise_groups <- function(string) {\n string <- gsub(" *[,] *", ",", string)\n string <- gsub("^\\\\s+|\\\\s+$", "", string)\n return(string)\n }\n \n # Function to make contrast contain valid R names\n-sanitiseContrast <- function(string) {\n- string <- strsplit(string, split="-")\n+sanitise_contrast <- function(string) {\n+ string <- strsplit(string, split = "-")\n string <- lapply(string, make.names)\n- string <- lapply(string, paste, collapse="-")\n+ string <- lapply(string, paste, collapse = "-")\n return(string)\n }\n \n # Function to change periods to whitespace in a string\n-unmake.names <- function(string) {\n- string <- gsub(".", " ", string, fixed=TRUE)\n+unmake_names <- function(string) {\n+ string <- gsub(".", " ", string, fixed = TRUE)\n return(string)\n }\n \n # Generate output folder and paths\n-makeOut <- function(filename) {\n+make_out <- function(filename) {\n return(paste0(opt$outPath, "/", filename))\n }\n \n # Generating design information\n-pasteListName <- function(string) {\n+paste_listname <- function(string) {\n return(paste0("factors$", string))\n }\n \n@@ -123,33 +123,33 @@\n }\n \n # Function to write code for html head and title\n-HtmlHead <- function(title) {\n+html_head <- function(title) {\n cata("<head>\\n")\n cata("<title>", title, "</title>\\n")\n cata("</head>\\n")\n }\n \n # Function to write code for html links\n-HtmlLink <- function(address, label=address) {\n+html_link <- function(address, label = address) {\n cata("<a href=\\"", address, "\\" target=\\"_blank\\">", label, "</a><br />\\n")\n }\n \n # Function to write code for html images\n-HtmlImage <- function(source, label=source, height=500, width=500) {\n+html_image <- function(source, label = source, height = 500, width = 500) {\n cata("<img src=\\"", source, "\\" alt=\\"", label, "\\" height=\\"", height)\n cata("\\" width=\\"", width, "\\"/>\\n")\n }\n \n # Function to write code for html list items\n-ListItem <- function(...) {\n+list_item <- function(...) {\n cata("<li>", ..., "</li>\\n")\n }\n \n-TableItem <- function(...) {\n+table_item <- function(...) {\n cata("<td>", ..., "</td>\\n")\n }\n \n-TableHeadItem <- function(...) {\n+table_head_item <- function(...) {\n cata("<th>", ..., "</th>\\n")\n }'..b'robust settings (robust = TRUE).")\n } else {\n- ListItem("eBayes was used with robust settings (robust=TRUE).")\n+ list_item("eBayes was used with robust settings (robust = TRUE).")\n }\n }\n-if (opt$pAdjOpt!="none") {\n- if (opt$pAdjOpt=="BH" || opt$pAdjOpt=="BY") {\n- tempStr <- paste0("MD Plot highlighted genes are significant at FDR ",\n- "of ", opt$pValReq," and exhibit log2-fold-change of at ",\n+if (opt$pAdjOpt != "none") {\n+ if (opt$pAdjOpt == "BH" || opt$pAdjOpt == "BY") {\n+ temp_str <- paste0("MD Plot highlighted genes are significant at FDR ",\n+ "of ", opt$pValReq, " and exhibit log2-fold-change of at ",\n "least ", opt$lfcReq, ".")\n- ListItem(tempStr)\n- } else if (opt$pAdjOpt=="holm") {\n- tempStr <- paste0("MD Plot highlighted genes are significant at adjusted ",\n- "p-value of ", opt$pValReq," by the Holm(1979) ",\n+ list_item(temp_str)\n+ } else if (opt$pAdjOpt == "holm") {\n+ temp_str <- paste0("MD Plot highlighted genes are significant at adjusted ",\n+ "p-value of ", opt$pValReq, " by the Holm(1979) ",\n "method, and exhibit log2-fold-change of at least ",\n opt$lfcReq, ".")\n- ListItem(tempStr)\n+ list_item(temp_str)\n }\n } else {\n- tempStr <- paste0("MD Plot highlighted genes are significant at p-value ",\n- "of ", opt$pValReq," and exhibit log2-fold-change of at ",\n+ temp_str <- paste0("MD Plot highlighted genes are significant at p-value ",\n+ "of ", opt$pValReq, " and exhibit log2-fold-change of at ",\n "least ", opt$lfcReq, ".")\n- ListItem(tempStr)\n+ list_item(temp_str)\n }\n cata("</ul>\\n")\n \n@@ -1231,21 +1232,21 @@\n \n cata("<table border=\\"1\\" cellpadding=\\"3\\">\\n")\n cata("<tr>\\n")\n-TableHeadItem("SampleID")\n-TableHeadItem(names(factors)[1]," (Primary Factor)")\n+table_head_item("SampleID")\n+table_head_item(names(factors)[1], " (Primary Factor)")\n \n if (ncol(factors) > 1) {\n for (i in names(factors)[2:length(names(factors))]) {\n- TableHeadItem(i)\n+ table_head_item(i)\n }\n cata("</tr>\\n")\n }\n \n-for (i in 1:nrow(factors)) {\n+for (i in seq_len(nrow(factors))) {\n cata("<tr>\\n")\n- TableHeadItem(row.names(factors)[i])\n- for (j in 1:ncol(factors)) {\n- TableItem(as.character(unmake.names(factors[i, j])))\n+ table_head_item(row.names(factors)[i])\n+ for (j in seq_len(ncol(factors))) {\n+ table_item(as.character(unmake_names(factors[i, j])))\n }\n cata("</tr>\\n")\n }\n@@ -1313,37 +1314,37 @@\n cata("<h4>limma</h4>\\n")\n cata(cit[3], "\\n")\n cata("<ol>\\n")\n-ListItem(cit[4])\n-ListItem(cit[10])\n-ListItem(cit[11])\n+list_item(cit[4])\n+list_item(cit[10])\n+list_item(cit[11])\n cata("</ol>\\n")\n \n cata("<h4>edgeR</h4>\\n")\n cata(cit[5], "\\n")\n cata("<ol>\\n")\n-ListItem(cit[6])\n-ListItem(cit[7])\n-ListItem(cit[8])\n-ListItem(cit[9])\n+list_item(cit[6])\n+list_item(cit[7])\n+list_item(cit[8])\n+list_item(cit[9])\n cata("</ol>\\n")\n \n cata("<p>Please report problems or suggestions to: su.s@wehi.edu.au</p>\\n")\n \n-for (i in 1:nrow(linkData)) {\n- if (grepl("session_info", linkData$Link[i])) {\n- HtmlLink(linkData$Link[i], linkData$Label[i])\n+for (i in seq_len(nrow(link_data))) {\n+ if (grepl("session_info", link_data$Link[i])) {\n+ html_link(link_data$Link[i], link_data$Label[i])\n }\n }\n \n cata("<table border=\\"0\\">\\n")\n cata("<tr>\\n")\n-TableItem("Task started at:"); TableItem(timeStart)\n+table_item("Task started at:"); table_item(time_start)\n cata("</tr>\\n")\n cata("<tr>\\n")\n-TableItem("Task ended at:"); TableItem(timeEnd)\n+table_item("Task ended at:"); table_item(time_end)\n cata("</tr>\\n")\n cata("<tr>\\n")\n-TableItem("Task run time:"); TableItem(timeTaken)\n+table_item("Task run time:"); table_item(time_taken)\n cata("<tr>\\n")\n cata("</table>\\n")\n \n' |
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| diff -r 0921444c832d -r 58c35179ebf0 limma_voom.xml --- a/limma_voom.xml Wed May 29 10:31:41 2019 -0400 +++ b/limma_voom.xml Fri Jun 04 20:37:04 2021 +0000 |
| [ |
| @@ -1,17 +1,27 @@ -<tool id="limma_voom" name="limma" version="3.38.3+galaxy3"> +<tool id="limma_voom" name="limma" version="3.48.0"> <description> Perform differential expression with limma-voom or limma-trend </description> + <xrefs> + <xref type="bio.tools">limma</xref> + </xrefs> + <edam_topics> + <edam_topic>topic_3308</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_3563</edam_operation> + <edam_operation>operation_3223</edam_operation> + </edam_operations> <requirements> - <requirement type="package" version="3.38.3">bioconductor-limma</requirement> - <requirement type="package" version="3.24.1">bioconductor-edger</requirement> - <requirement type="package" version="1.4.30">r-statmod</requirement> - <requirement type="package" version="1.0.0">r-scales</requirement> + <requirement type="package" version="3.48.0">bioconductor-limma</requirement> + <requirement type="package" version="3.34.0">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="0.2.20">r-rjson</requirement> - <requirement type="package" version="1.20.2">r-getopt</requirement> - <requirement type="package" version="3.0.1">r-gplots</requirement> - <requirement type="package" version="1.10.0">bioconductor-glimma</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="2.2.0">bioconductor-glimma</requirement> </requirements> <version_command><![CDATA[ |