# HG changeset patch
# User iuc
# Date 1680596751 0
# Node ID df929f2571796b8d47d1f3ee7117389f26e5caf0
# Parent  b47c006d90c55648121a481a042c0f589b834cde
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140

diff -r b47c006d90c5 -r df929f257179 dexseq.R
--- a/dexseq.R	Tue May 03 20:23:18 2022 +0000
+++ b/dexseq.R	Tue Apr 04 08:25:51 2023 +0000
@@ -1,6 +1,7 @@
 ## Setup R error handling to go to stderr
-options(show.error.messages = F, error = function() {
-    cat(geterrmessage(), file = stderr()); q("no", 1, F)
+options(show.error.messages = FALSE, error = function() {
+    cat(geterrmessage(), file = stderr())
+    q("no", 1, FALSE)
 })
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
@@ -27,14 +28,14 @@
     "factors", "f", 1, "character",
     "threads", "p", 1, "integer",
     "fdr", "c", 1, "double"
-), byrow = TRUE, ncol = 4);
-opt <- getopt(spec);
+), byrow = TRUE, ncol = 4)
+opt <- getopt(spec)
 
 # if help was asked for print a friendly message
 # and exit with a non-zero error code
 if (!is.null(opt$help)) {
-    cat(getopt(spec, usage = TRUE));
-    q(status = 1);
+    cat(getopt(spec, usage = TRUE))
+    q(status = 1)
 }
 
 trim <- function(x) gsub("^\\s+|\\s+$", "", x)
@@ -110,7 +111,8 @@
 for (i in seq_len(nrow(export_table))) {
   export_table[i, last_column] <- paste(export_table[i, last_column][[1]], collapse = ", ")
 }
-write.table(export_table, file = opt$outfile, sep = "\t", quote = FALSE, col.names = FALSE)
+export_table[, c(last_column)] <- sapply(export_table[, c(last_column)], as.character)
+write.table(export_table, file = opt$outfile, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
 print("Written Results")
 
 if (!is.null(opt$rds)) {
diff -r b47c006d90c5 -r df929f257179 dexseq.xml
--- a/dexseq.xml	Tue May 03 20:23:18 2022 +0000
+++ b/dexseq.xml	Tue Apr 04 08:25:51 2023 +0000
@@ -1,15 +1,10 @@
-<tool id="dexseq" name="DEXSeq" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="dexseq" name="DEXSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Determines differential exon usage from count tables</description>
-    <xrefs>
-        <xref type="bio.tools">dexseq</xref>
-    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="1.20.2">r-getopt</requirement>
-        <requirement type="package" version="0.2.20">r-rjson</requirement>
-    </expand>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <code file="dexseq_helper.py" />
     <stdio>
         <regex match="Execution halted"
@@ -102,7 +97,11 @@
         <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/>
     </inputs>
     <outputs>
-        <data name="dexseq_out" format="tabular" label="${tool.name} on ${on_string}: result" />
+        <data name="dexseq_out" format="tabular" label="${tool.name} on ${on_string}: result">
+            <actions>
+                <action name="column_names" type="metadata" default="GeneID,ExonID,Exon base mean,Dispersion,Stat,p-value,p-adj,X1_group1,X2_group2,log2(FC),Chr. name,Start,End,Width,Strand,Raw counts"/>
+            </actions>
+        </data>
         <data name="htmlreport" format="html" label="${tool.name} on ${on_string}: report">
             <filter>report is True</filter>
         </data>
diff -r b47c006d90c5 -r df929f257179 dexseq_count.xml
--- a/dexseq_count.xml	Tue May 03 20:23:18 2022 +0000
+++ b/dexseq_count.xml	Tue Apr 04 08:25:51 2023 +0000
@@ -1,13 +1,10 @@
-<tool id="dexseq_count" name="DEXSeq-Count" version="@TOOL_VERSION@.1" profile="@PROFILE@">
+<tool id="dexseq_count" name="DEXSeq-Count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Prepare and count exon abundancies from RNA-seq data</description>
-    <xrefs>
-        <xref type="bio.tools">dexseq</xref>
-    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-    </expand>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
@@ -32,6 +29,8 @@
         $mode.flattened_gtf_in
         '$mode.bamfile'
         '$counts_file'
+    &&
+    sed -i 's/\"//g' '$counts_file'
 #end if
     ]]></command>
     <inputs>
diff -r b47c006d90c5 -r df929f257179 macros.xml
--- a/macros.xml	Tue May 03 20:23:18 2022 +0000
+++ b/macros.xml	Tue Apr 04 08:25:51 2023 +0000
@@ -1,13 +1,21 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.28.1</token>
-    <token name="@PROFILE@">21.01</token>
+    <token name="@TOOL_VERSION@">1.44</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">22.01</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-dexseq</requirement>
-            <yield />
+            <requirement type="package" version="1.20.3">r-getopt</requirement>
+            <requirement type="package" version="0.2.21">r-rjson</requirement>
         </requirements>
     </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">dexseq</xref>
+            <xref type="bioconductor">dexseq</xref>
+        </xrefs>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1101/gr.133744.111</citation>
diff -r b47c006d90c5 -r df929f257179 plotdexseq.R
--- a/plotdexseq.R	Tue May 03 20:23:18 2022 +0000
+++ b/plotdexseq.R	Tue Apr 04 08:25:51 2023 +0000
@@ -1,6 +1,7 @@
 ## Setup R error handling to go to stderr
-options(show.error.messages = F, error = function() {
-    cat(geterrmessage(), file = stderr()); q("no", 1, F)
+options(show.error.messages = FALSE, error = function() {
+    cat(geterrmessage(), file = stderr())
+    q("no", 1, FALSE)
 })
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
@@ -25,8 +26,8 @@
     "names", "a", 1, "logical",
     "normcounts", "n", 1, "logical",
     "splicing", "s", 1, "logical"
-), byrow = TRUE, ncol = 4);
-opt <- getopt(spec);
+), byrow = TRUE, ncol = 4)
+opt <- getopt(spec)
 
 res <- readRDS(opt$rdata)
 
diff -r b47c006d90c5 -r df929f257179 plotdexseq.xml
--- a/plotdexseq.xml	Tue May 03 20:23:18 2022 +0000
+++ b/plotdexseq.xml	Tue Apr 04 08:25:51 2023 +0000
@@ -1,14 +1,10 @@
-<tool id="plotdexseq" name="plotDEXSeq" version="@TOOL_VERSION@.1" profile="@PROFILE@">
+<tool id="plotdexseq" name="plotDEXSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Visualization of the per gene DEXSeq results</description>
-    <xrefs>
-        <xref type="bio.tools">dexseq</xref>
-    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="1.20.2">r-getopt</requirement>
-    </expand>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <version_command><![CDATA[
 echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")"
     ]]></version_command>