Mercurial > repos > iuc > masigpro

changeset 4:402e0b9cfd87 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 7dc16d5d4169a8fbfb3fad3b2212fd8b6d481f5f"
author iuc
date Sat, 27 Nov 2021 09:58:07 +0000
parents 83f8b5ceff43
children
files masigpro.R masigpro.xml
diffstat 2 files changed, 68 insertions(+), 61 deletions(-) [+]
line wrap: on
line diff
--- a/masigpro.R	Tue Dec 03 06:18:47 2019 -0500
+++ b/masigpro.R	Sat Nov 27 09:58:07 2021 +0000
@@ -6,7 +6,11 @@
 # wrapper as a basis to build upon.
 
 # setup R error handling to go to stderr
-options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+error_foo <- function() {
+  cat(geterrmessage(), file = stderr());
+  q("no", 1, F)
+}
+options(show.error.messages = F, error = error_foo)
 
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
@@ -18,42 +22,40 @@
 })
 
 # The following code fixes an error in the stepback function
-# of the maSigPro package. This code is hopefully temporary 
-# and can be removed if the fix is included in a future 
+# of the maSigPro package. This code is hopefully temporary
+# and can be removed if the fix is included in a future
 # version. The stepback function in the maSigPro namespace
 # will be overwritten by the following function.
-stepback <- function (y = y, d = d, alfa = 0.05, family = gaussian() , epsilon=0.00001) 
-{
-    lm1 <- glm(y ~ ., data = d, family=family, epsilon=epsilon)
+stepback <- function(y = y, d = d, alfa = 0.05, family = gaussian(), epsilon=0.00001) {
+    lm1 <- glm(y ~ ., data = d, family = family, epsilon = epsilon)
     result <- summary(lm1)
     max <- max(result$coefficients[, 4][-1], na.rm = TRUE)
     if (length(result$coefficients[, 4][-1]) == 1) {
       if (max > alfa) {
-        max = 0 
-        lm1 <- glm(y ~ 1,  family=family, epsilon=epsilon)
+        max <- 0
+        lm1 <- glm(y ~ 1,  family = family, epsilon = epsilon)
       }
     }
     while (max > alfa) {
-        varout <- names(result$coefficients[, 4][-1])[result$coefficients[, 
-            4][-1] == max][1]
+        varout <- names(result$coefficients[, 4][-1])[result$coefficients[, 4][-1] == max][1]
         pos <- position(matrix = d, vari = varout)
         d <- d[, -pos]
         if (length(result$coefficients[, 4][-1]) == 2) {
             min <- min(result$coefficients[, 4][-1], na.rm = TRUE)
-            lastname <- names(result$coefficients[, 4][-1])[result$coefficients[,4][-1] == min]
+            lastname <- names(result$coefficients[, 4][-1])[result$coefficients[, 4][-1] == min]
         }
         if (is.null(dim(d))) {
             d <- as.data.frame(d)
             colnames(d) <- lastname
         }
-        lm1 <- glm(y ~ ., data = d, family=family, epsilon=epsilon)
+        lm1 <- glm(y ~ ., data = d, family = family, epsilon = epsilon)
         result <- summary(lm1)
         max <- max(result$coefficients[, 4][-1], na.rm = TRUE)
         if (length(result$coefficients[, 4][-1]) == 1) {
             max <- result$coefficients[, 4][-1]
             if (max > alfa) {
-                max = 0
-                lm1 <- glm(y ~ 1,  family=family, epsilon=epsilon)
+                max <- 0
+                lm1 <- glm(y ~ 1,  family = family, epsilon = epsilon)
             }
         }
     }
@@ -61,7 +63,7 @@
 }
 
 unlockBinding("stepback", as.environment("package:maSigPro"))
-assignInNamespace("stepback", stepback, ns="maSigPro", envir=as.environment("package:maSigPro"))
+assignInNamespace("stepback", stepback, ns = "maSigPro", envir = as.environment("package:maSigPro"))
 assign("stepback", stepback, as.environment("package:maSigPro"))
 lockBinding("stepback", as.environment("package:maSigPro"))
 # End of temporary code to fix stepback.R
@@ -74,52 +76,52 @@
 # make_option(c("-h", "--help"), action="store_true", default=FALSE,
 # help="Show this help message and exit")
 option_list <- list(
- make_option(c("-q", "--quiet"), action="store_false",
- dest="verbose", help="Print little output"),
- make_option(c("-e", "--edesign"), type="character"),
- make_option(c("-d", "--data"), type="character"),
- make_option(c("-o", "--outfile"), type="character"),
- make_option("--degree", type="integer", default=1),
- make_option("--time_col", type="integer", default=1),
- make_option("--repl_col", type="integer", default=2),
- make_option("--qvalue", type="double", default=0.05),
- make_option("--min_obs", type="integer", default=6),
- make_option("--step_method", type="character", default="backward"),
- make_option("--nvar_correction", type="logical", default=FALSE),
- make_option("--alfa", type="double", default=0.05),
- make_option("--rsq", type="double", default=0.7),
- make_option("--vars", type="character", default="groups"),
- make_option("--significant_intercept", type="character", default="dummy"),
- make_option("--cluster_data", type="integer", default=1),
- make_option(c("-k", "--k"), type="integer", default=9),
- make_option("--print_cluster", type="logical", default=FALSE),
- make_option("--cluster_method", type="character", default="hclust"),
- make_option("--distance", type="character", default="cor"),
- make_option("--agglo_method", type="character", default="ward.D"),
- make_option("--iter_max", type="integer", default=500),
- make_option("--color_mode", type="character", default="rainbow"),
- make_option("--show_fit", type="logical", default=TRUE),
- make_option("--show_lines", type="logical", default=TRUE),
- make_option("--cexlab", type="double", default=0.8),
- make_option("--legend", type="logical", default=TRUE)
+ make_option(c("-q", "--quiet"), action = "store_false",
+ dest = "verbose", help = "Print little output"),
+ make_option(c("-e", "--edesign"), type = "character"),
+ make_option(c("-d", "--data"), type = "character"),
+ make_option(c("-o", "--outfile"), type = "character"),
+ make_option("--degree", type = "integer", default = 1),
+ make_option("--time_col", type = "integer", default = 1),
+ make_option("--repl_col", type = "integer", default = 2),
+ make_option("--qvalue", type = "double", default = 0.05),
+ make_option("--min_obs", type = "integer", default = 6),
+ make_option("--step_method", type = "character", default = "backward"),
+ make_option("--nvar_correction", type = "logical", default = FALSE),
+ make_option("--alfa", type = "double", default = 0.05),
+ make_option("--rsq", type = "double", default = 0.7),
+ make_option("--vars", type = "character", default = "groups"),
+ make_option("--significant_intercept", type = "character", default = "dummy"),
+ make_option("--cluster_data", type = "integer", default = 1),
+ make_option(c("-k", "--k"), type = "integer", default = 9),
+ make_option("--print_cluster", type = "logical", default = FALSE),
+ make_option("--cluster_method", type = "character", default = "hclust"),
+ make_option("--distance", type = "character", default = "cor"),
+ make_option("--agglo_method", type = "character", default = "ward.D"),
+ make_option("--iter_max", type = "integer", default = 500),
+ make_option("--color_mode", type = "character", default = "rainbow"),
+ make_option("--show_fit", type = "logical", default = TRUE),
+ make_option("--show_lines", type = "logical", default = TRUE),
+ make_option("--cexlab", type = "double", default = 0.8),
+ make_option("--legend", type = "logical", default = TRUE)
 )
 
 # get command line options, if help option encountered print help and exit,
 # otherwise if options not found on command line then set defaults
-opt <- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 
 # enforce the following required arguments
 if (is.null(opt$edesign)) {
   cat("'edesign' is required\n")
-  q(status=1)
+  q(status = 1)
 }
 if (is.null(opt$data)) {
   cat("'data' is required\n")
-  q(status=1)
+  q(status = 1)
 }
 if (is.null(opt$outfile)) {
   cat("'outfile' is required\n")
-  q(status=1)
+  q(status = 1)
 }
 
 verbose <- if (is.null(opt$quiet)) {
@@ -128,9 +130,9 @@
   FALSE
 }
 
-edesign <- as.matrix(read.table(opt$edesign, header=TRUE, row.names = 1))
+edesign <- as.matrix(read.table(opt$edesign, header = TRUE, row.names = 1))
 
-data <- read.table(opt$data, header=TRUE, check.names=FALSE)
+data <- read.table(opt$data, header = TRUE, check.names = FALSE)
 
 results <- maSigPro(data, edesign, degree = opt$degree, time.col = opt$time_col,
          repl.col = opt$repl_col, Q = opt$qvalue, min.obs = opt$min_obs,
@@ -145,20 +147,18 @@
          legend = opt$legend)
 
 if (opt$print_cluster) {
-    for (i in 1:length(results$sig.genes)) {
-    
-    colname <- paste(names(results$sig.genes)[i], "cluster", sep = "_")
-    
-    results$summary[colname] <- ""
-    results$summary[[colname]][1:length(results$sig.genes[[i]]$sig.profiles$`cluster$cut`)] <-
-        results$sig.genes[[i]]$sig.profiles$`cluster$cut`
+    for (i in seq_len(length(results$sig.genes))) {
+      colname <- paste(names(results$sig.genes)[i], "cluster", sep = "_")
+      results$summary[colname] <- ""
+      results$summary[[colname]][seq_len(length(results$sig.genes[[i]]$sig.profiles$`cluster$cut`))] <-
+          results$sig.genes[[i]]$sig.profiles$`cluster$cut`
     }
 }
 
 filename <- opt$outfile
 
-write.table((results$summary), file=filename, sep="\t", quote=FALSE,
-            row.names=FALSE, col.names=TRUE)
+write.table((results$summary), file = filename, sep = "\t", quote = FALSE,
+            row.names = FALSE, col.names = TRUE)
 
 cat("Session information:\n\n")
 
--- a/masigpro.xml	Tue Dec 03 06:18:47 2019 -0500
+++ b/masigpro.xml	Sat Nov 27 09:58:07 2021 +0000
@@ -1,8 +1,16 @@
-<tool id="masigpro" name="maSigPro" version="1.49.3.1+galaxy1">
+<!-- TODO remove .1 in tool version with next update -->
+<tool id="masigpro" name="maSigPro" version="@TOOL_VERSION@.1+galaxy@VERSION_SUFFIX@">
     <description>Significant Gene Expression Profile Differences in Time Course Gene Expression Data</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.49.3</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>        
+    <xrefs>
+        <xref type="bio.tools">masigpro</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="8.25">coreutils</requirement>
-        <requirement type="package" version="1.49.3">bioconductor-masigpro</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-masigpro</requirement>
         <requirement type="package" version="1.3.2">r-optparse</requirement>
         <requirement type="package" version="4.4">sed</requirement>
     </requirements>
@@ -385,7 +393,6 @@
                 <param name="time" value="3" />
                 <param name="files" value="control_3H.counts,treat_3H_1.counts,treat_3H_2.counts" />
             </repeat>
-            <param name="replicates_selector" value="advanced" />
             <repeat name="rep_repl">
                 <param name="files" value="treat_3H_1.counts,treat_3H_2.counts" />
             </repeat>