| Previous changeset 7:334ce9b1bac5 (2019-08-08) Next changeset 9:6e53e565fc6a (2021-06-26) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" |
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modified:
edger.R edger.xml |
| b |
| diff -r 334ce9b1bac5 -r 3d89af8a44f0 edger.R --- a/edger.R Thu Aug 08 06:44:11 2019 -0400 +++ b/edger.R Thu Jun 03 19:34:18 2021 +0000 |
| [ |
| b'@@ -7,23 +7,23 @@\n # filesPath", "j", 2, "character" -JSON list object if multiple files input\n # matrixPath", "m", 2, "character" -Path to count matrix\n # factFile", "f", 2, "character" -Path to factor information file\n-# factInput", "i", 2, "character" -String containing factors if manually input \n+# factInput", "i", 2, "character" -String containing factors if manually input\n # annoPath", "a", 2, "character" -Path to input containing gene annotations\n # contrastData", "C", 1, "character" -String containing contrasts of interest\n # cpmReq", "c", 2, "double" -Float specifying cpm requirement\n # cntReq", "z", 2, "integer" -Integer specifying minimum total count requirement\n # sampleReq", "s", 2, "integer" -Integer specifying cpm requirement\n-# normCounts", "x", 0, "logical" -String specifying if normalised counts should be output \n+# normCounts", "x", 0, "logical" -String specifying if normalised counts should be output\n # rdaOpt", "r", 0, "logical" -String specifying if RData should be output\n-# lfcReq", "l", 1, "double" -Float specifying the log-fold-change requirement \n+# lfcReq", "l", 1, "double" -Float specifying the log-fold-change requirement\n # pValReq", "p", 1, "double" -Float specifying the p-value requirement\n-# pAdjOpt", "d", 1, "character" -String specifying the p-value adjustment method \n-# normOpt", "n", 1, "character" -String specifying type of normalisation used \n-# robOpt", "b", 0, "logical" -String specifying if robust options should be used \n-# lrtOpt", "t", 0, "logical" -String specifying whether to perform LRT test instead \n+# pAdjOpt", "d", 1, "character" -String specifying the p-value adjustment method\n+# normOpt", "n", 1, "character" -String specifying type of normalisation used\n+# robOpt", "b", 0, "logical" -String specifying if robust options should be used\n+# lrtOpt", "t", 0, "logical" -String specifying whether to perform LRT test instead\n #\n-# OUT: \n-# MDS Plot \n+# OUT:\n+# MDS Plot\n # BCV Plot\n # QL Plot\n # MD Plot\n@@ -37,108 +37,112 @@\n # Modified by: Maria Doyle - Oct 2017 (some code taken from the DESeq2 wrapper)\n \n # Record starting time\n-timeStart <- as.character(Sys.time())\n+time_start <- as.character(Sys.time())\n \n # setup R error handling to go to stderr\n-options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )\n+options(show.error.messages = F, error = function() {\n+ cat(geterrmessage(), file = stderr())\n+ q("no", 1, F)\n+})\n \n # we need that to not crash galaxy with an UTF8 error on German LC settings.\n loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")\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(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 \n ################################################################################\n ### Function Delcaration\n ################################################################################\n # Function to sanitise contrast equations so there are no whitespaces\n '..b' } else {\n- ListItem("The edgeR quasi-likelihood test was used.")\n- }\n+ if (want_robust) {\n+ list_item("The edgeR quasi-likelihood test was used with robust settings (robust=TRUE with estimateDisp and glmQLFit).")\n+ } else {\n+ list_item("The edgeR quasi-likelihood test was used.")\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- "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$pValReq," by the Holm(1979) ",\n- "method, and exhibit log2-fold-change of at least ", \n- opt$lfcReq, ".")\n- ListItem(tempStr)\n- }\n+if (opt$pAdjOpt != "none") {\n+ if (opt$pAdjOpt == "BH" || opt$pAdjOpt == "BY") {\n+ temp_str <- paste0(\n+ "MD-Plot highlighted genes are significant at FDR ",\n+ "of ", opt$pValReq, " and exhibit log2-fold-change of at ",\n+ "least ", opt$lfcReq, "."\n+ )\n+ list_item(temp_str)\n+ } else if (opt$pAdjOpt == "holm") {\n+ temp_str <- paste0(\n+ "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+ )\n+ list_item(temp_str)\n+ }\n } else {\n- tempStr <- paste0("MD-Plot highlighted genes are significant at p-value ",\n- "of ", opt$pValReq," and exhibit log2-fold-change of at ", \n- "least ", opt$lfcReq, ".")\n- ListItem(tempStr)\n+ temp_str <- paste0(\n+ "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+ )\n+ list_item(temp_str)\n }\n cata("</ul>\\n")\n \n@@ -711,41 +738,44 @@\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- }\n- cata("</tr>\\n")\n- }\n+if (ncol(factors) > 1) {\n+ for (i in names(factors)[2:length(names(factors))]) {\n+ table_head_item(i)\n+ }\n+ cata("</tr>\\n")\n+}\n \n-for (i in 1: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- }\n- cata("</tr>\\n")\n+for (i in seq_len(nrow((factors)))) {\n+ cata("<tr>\\n")\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 cata("</table>")\n \n-for (i in 1:nrow(linkData)) {\n- if (grepl("session_info", linkData$Link[i])) {\n- HtmlLink(linkData$Link[i], linkData$Label[i])\n- }\n+for (i in seq_len(nrow(link_data))) {\n+ if (grepl("session_info", link_data$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:")\n+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:")\n+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:")\n+table_item(time_taken)\n cata("<tr>\\n")\n cata("</table>\\n")\n \n' |
| b |
| diff -r 334ce9b1bac5 -r 3d89af8a44f0 edger.xml --- a/edger.xml Thu Aug 08 06:44:11 2019 -0400 +++ b/edger.xml Thu Jun 03 19:34:18 2021 +0000 |
| [ |
| @@ -1,16 +1,26 @@ -<tool id="edger" name="edgeR" version="3.24.1+galaxy1"> +<tool id="edger" name="edgeR" version="3.34.0"> <description> Perform differential expression of count data </description> + <xrefs> + <xref type="bio.tools">edger</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="3.24.1">bioconductor-edger</requirement> - <requirement type="package" version="3.38.3">bioconductor-limma</requirement> + <requirement type="package" version="3.34.0">bioconductor-edger</requirement> + <requirement type="package" version="3.48.0">bioconductor-limma</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="1.4.30">r-statmod</requirement> + <requirement type="package" version="1.20.3">r-getopt</requirement> + <requirement type="package" version="1.4.36">r-statmod</requirement> <!-- required for alpha function used with plotMD --> - <requirement type="package" version="1.0.0">r-scales</requirement> + <requirement type="package" version="1.1.1">r-scales</requirement> </requirements> <version_command><![CDATA[ |