# HG changeset patch
# User siwaa
# Date 1726569699 0
# Node ID 2af4b1e46d9016da01f87d69c85745ffe4bc8b38
# Parent  5fdc9d0c223bb9ae34f112ef25aa494694b92d4a
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/0376c8590ba7b401f91db9be50a49e03cf5044fb/toos/CarboSeqSimulator commit 0376c8590ba7b401f91db9be50a49e03cf5044fb-dirty"

diff -r 5fdc9d0c223b -r 2af4b1e46d90 carboseqSimulator.xml
--- a/carboseqSimulator.xml	Fri Aug 30 13:29:48 2024 +0000
+++ b/carboseqSimulator.xml	Tue Sep 17 10:41:39 2024 +0000
@@ -1,7 +1,7 @@
-<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.14">
+<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.15">
   <description>To run the CarboSeq simulator</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:siwaa</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:main</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
   (env | grep DOCKER_IMAGE) &&
@@ -32,7 +32,7 @@
       <param name="semantifier" value="modeltoolbox_sem_local" />
       <output name="output" ftype="rdata" >
       	<assert_contents>
-	  <has_size value="38654" negate="false" />
+	  <has_size value="1202" negate="false" />
 	  <has_size value="0" negate="true" />
 	</assert_contents>
       </output>
@@ -42,7 +42,7 @@
       <param name="semantifier" value="modeltoolbox_sem_remote" />
       <output name="output" ftype="rdata" >
       	<assert_contents>
-	  <has_size value="38654" negate="false" />
+	  <has_size value="1202" negate="false" />
 	  <has_size value="0" negate="true" />
 	</assert_contents>
       </output>
diff -r 5fdc9d0c223b -r 2af4b1e46d90 carboseqUnsplit.R
--- a/carboseqUnsplit.R	Fri Aug 30 13:29:48 2024 +0000
+++ b/carboseqUnsplit.R	Tue Sep 17 10:41:39 2024 +0000
@@ -1,23 +1,13 @@
-
-resU <- data.frame()
+library(data.table)
+library(dplyr)
 
-listFiles <- list.files('./inputs')
-
-# restoring the order first
-
-orderVec <- c()
+resU <- data.table();
 
-for (i in list.files('./inputs')) {
-    load(file.path('.', 'inputs',i))
-    orderVec <- c(orderVec, res$ID[1]);
-    rm(res)
-    }
+listFiles <- commandArgs(trailingOnly = TRUE)
 
-listFilesReOrder <- listFiles[order(orderVec)]
-
-for (i in listFilesReOrder) {
-    load(file.path('.', 'inputs',i))
-    resU<- rbind(resU, res);
+for (i in listFiles) {
+    load(i)
+    resU<- dplyr::bind_rows(resU, res);
     rm(res)
     }
 
diff -r 5fdc9d0c223b -r 2af4b1e46d90 carboseqUnsplit.xml
--- a/carboseqUnsplit.xml	Fri Aug 30 13:29:48 2024 +0000
+++ b/carboseqUnsplit.xml	Tue Sep 17 10:41:39 2024 +0000
@@ -1,14 +1,10 @@
-<tool id="CarboSeqUnsplit" name="CarboSeqUnsplit" version="1.0.3">
+<tool id="CarboSeqUnsplit" name="CarboSeqUnsplit" version="1.0.4">
   <description>To unsplit CarboSeq results</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:siwa</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/carboseq/record-projet-carboseq/carboseq_r_4_siwaa</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
-  mkdir inputs &&
-  #for $input in $inputList
-  cp $input inputs &&
-  #end for
-  Rscript $__tool_directory__/carboseqUnsplit.R &&
+  Rscript $__tool_directory__/carboseqUnsplit.R #for $input in $inputList# $input #end for# &&
   cp csopraRes.Rdata $output
     ]]>
   </command>