# HG changeset patch
# User siwaa
# Date 1685610791 0
# Node ID 21e91d3b7068380a185db1cbf92bbd6294315252

"planemo upload for repository https://forgemia.inra.fr/redelac"

diff -r 000000000000 -r 21e91d3b7068 REDELACparallelSticsRsequence-10.0.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/REDELACparallelSticsRsequence-10.0.xml	Thu Jun 01 09:13:11 2023 +0000
@@ -0,0 +1,51 @@
+<tool id="REDELACparallelSticsRsequence-10.0.0" name="redelacparallelsticsrsequence-10.0.0" version="1.0.0">
+  <description>to run sequences paralelly 4 REDELAC[Stics-10.0.0]</description>
+  <requirements>
+    <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics_redelac:10.0.0</container>
+  </requirements>
+  <command detect_errors="aggressive">
+    <![CDATA[ 
+	     cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/JavaSTICS-1.5.1-STICS-10.0.0 . &&
+	     unzip ${WorkSpace} -d TMP &&
+             export WSname=\$(ls TMP) &&
+	     mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
+	     cp ${SuccessionPlan} JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv &&
+	     cd JavaSTICS-1.5.1-STICS-10.0.0 &&
+	     Rscript --verbose $__tool_directory__/REDELACparallelSticsRsequence.R &&
+             mv WS \$WSname &&
+	     zip -r \$WSname \$WSname &&
+	     cp \$WSname.zip ${SimulatedWorkspace} &&
+	     cp results.RData ${SimulationResults}
+     ]]>
+  </command>
+  <inputs>
+    <param name="WorkSpace" type="data" format="zip" label="Select a stics Workspace(zip file)"/>
+    <param name="SuccessionPlan" type="data" format="csv" label="Select a plan (xlsx)"/>
+  </inputs>
+  <outputs>
+    <data format="zip" name="SimulatedWorkspace"
+          label="Stics simulated  Workspace">
+    </data>
+    <data format="rdata" name="SimulationResults"
+          label="Stics simulations results">
+    </data>
+  </outputs>
+  <tests>
+  </tests>
+  <help>
+*The usage of this tool is restricted to the user of the stics_authorized group.*
+
+*To be granted, apply to the Project Stics Team and then request to SIWAA*
+
+Documentation
+-------------
+A tool to simulate stics rotation paralelly
+
+Credits
+-------
+-  Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team
+-  Stics Site: https://www6.paca.inra.fr/stics_eng
+-  Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
+-  Copyright: INRAE
+  </help>
+</tool>
diff -r 000000000000 -r 21e91d3b7068 REDELACparallelSticsRsequence.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/REDELACparallelSticsRsequence.R	Thu Jun 01 09:13:11 2023 +0000
@@ -0,0 +1,77 @@
+library(SticsRFiles)
+library(SticsOnR)
+library(parallel)
+library(doParallel)
+library(readxl)
+
+workspace <- paste0(getwd(), "/WS")
+javastics_path <- getwd()
+default_config_path <- paste0(javastics_path, "/config")
+
+# copy of the var.mod and rap.mod into the config folder
+# generalizing maybe should be inside a config folder
+
+#file.copy(from = file.path(workspace, "var.mod"),
+#          to = file.path(default_config_path, "var.mod"),
+#	  overwrite = TRUE)
+#file.copy(from = file.path(workspace, "rap.mod"),
+#          to = file.path(default_config_path, "rap.mod"),
+#	  overwrite = TRUE)
+
+txt_path <- paste0(getwd(), "/WS/txt_files")
+#dir.create(txt_path,recursive = T)
+
+#gen_usms_xml2txt(javastics = javastics_path,
+#                 workspace = workspace,
+#		 out_dir = txt_path,
+#		 check = FALSE)
+
+print("==================================")
+
+print(paste0("Cores=", detectCores()))
+print(paste0("javastics=", javastics_path))
+print(paste0("ws=", workspace))
+print(paste0("out_dir=", txt_path))
+
+print("==================================")
+
+
+# List of successive USMs
+successive_usms_file <- ("successionPlan.csv")
+successive_usms_tab <- read.csv(file = file.path(workspace, successive_usms_file))
+
+no_cores <- detectCores() - 1  
+cl <- makeCluster(no_cores)  
+registerDoParallel(cl)
+
+result <- foreach(i=1:nrow(successive_usms_tab),
+                  .packages = c("SticsRFiles", "SticsOnR") ) %dopar% {
+  
+  nusms <- as.numeric(successive_usms_tab[i,2])
+  
+  vec <- as.character(successive_usms_tab[i,c(3:(2+nusms))])
+  
+  list_successive_usms <- list(vec)
+  
+  sim_options <- stics_wrapper_options(javastics = javastics_path, 
+                                       stics_exe = paste0(javastics_path,"/bin/stics_modulo"),
+                                       workspace = txt_path, 
+                                       verbose = TRUE, 
+                                       successive = list_successive_usms)
+  list_usms <- vec
+  
+  stics_wrapper(model_options = sim_options, situation = list_usms)
+                  }
+
+stopCluster(cl)  
+
+for (i in 1:nrow(successive_usms_tab)) { #i=1
+  if (i == 1) {
+    simPCP <- result[[i]]
+  } else {
+    simPCP$sim_list <- c(simPCP$sim_list, result[[i]]$sim_list)
+  }
+
+}
+
+save(simPCP, file = "results.RData")
\ No newline at end of file