# HG changeset patch
# User siwaa
# Date 1706035894 0
# Node ID 4d0807472ad3b2b930a0560cddaec159708568dc
# Parent  f2fe11a203718c2135a123973f14d6bdec0bfc41
"planemo upload for repository https://forgemia.inra.fr/redelac commit 9c5802d9b947f1e59bd5df610ebe5dfc89745be6"

diff -r f2fe11a20371 -r 4d0807472ad3 redelacSticsInputGenerator.R
--- a/redelacSticsInputGenerator.R	Mon Jan 22 15:15:07 2024 +0000
+++ b/redelacSticsInputGenerator.R	Tue Jan 23 18:51:34 2024 +0000
@@ -78,8 +78,10 @@
 
 if (parallel) {
   doFuture::registerDoFuture()
-
-  future::plan(multicore, workers = nbSlots)
+  future::plan(multisession, workers = nbSlots)
+  `%dordopar%` <- `%dofuture%`
+} else {
+  `%dordopar%` <- `%do%`
 }
 
 beforeGenXmlTime <- Sys.time()
@@ -93,7 +95,7 @@
 ids <- seq(1, nbUSMs, chunckSize)
 
 foreach (i = ids,
-         .options.future = list(packages = c("foreach", "SticsRFiles"))) %dofuture% {
+         .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
            gen_usms_xml(file = file.path(workspace, paste0("usms__", i, ".xml")),
                         param_df = usms_param[i:min(i + chunckSize - 1, nbUSMs),])
          }
@@ -106,7 +108,7 @@
 beforeGenTxtTime <- Sys.time()
 
 foreach (i = ids,
-         .options.future = list(packages = c("foreach", "SticsRFiles"))) %dofuture% {
+         .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
            gen_usms_xml2txt(
              javastics = javastics_path,
              workspace = workspace,
diff -r f2fe11a20371 -r 4d0807472ad3 redelacSticsInputGenerator.bash
--- a/redelacSticsInputGenerator.bash	Mon Jan 22 15:15:07 2024 +0000
+++ b/redelacSticsInputGenerator.bash	Tue Jan 23 18:51:34 2024 +0000
@@ -27,9 +27,9 @@
 echo "=================================" && 
 cat ./bashlog &&
 echo "=================================" && 
-rm WS/1* &&
+(cd WS && ls | grep -e '^[0-9]*\.[0-9]*$' | xargs -i rm {}) &&
 mv WS $WSname &&
-/usr/bin/time -p -o ./bashlog zip ${13} -q -r $WSname $WSname &&
+/usr/bin/time -p -o ./bashlog zip ${13} -y -q -r $WSname $WSname &&
 echo "Step 2, time to zip the Workspace:" &&
 echo "==================================" && 
 cat ./bashlog &&
diff -r f2fe11a20371 -r 4d0807472ad3 redelacSticsInputGenerator.xml
--- a/redelacSticsInputGenerator.xml	Mon Jan 22 15:15:07 2024 +0000
+++ b/redelacSticsInputGenerator.xml	Tue Jan 23 18:51:34 2024 +0000
@@ -1,7 +1,7 @@
-<tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.9">
+<tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.10">
   <description>to run generate Stics Inputs for REDELAC</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:34ec8256987dc39507f0679d110c6306b00d5890</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:5d8a06fbf5783ca65fba694dbeb5d2749020c36d</container>
   </requirements>
   <command detect_errors="aggressive">
     <![CDATA[