# HG changeset patch
# User siwaa
# Date 1635161551 0
# Node ID f1070dc2446c4eee4fb44f80ea240acc30c309c5

"planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"

diff -r 000000000000 -r f1070dc2446c stics4carsolel.bash
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stics4carsolel.bash	Mon Oct 25 11:32:31 2021 +0000
@@ -0,0 +1,26 @@
+echo "Stics4CarSolEl Job starting:"
+date;
+
+n_slots=${1};
+csv_plan=${2};
+sim_number=$(($(cat ${csv_plan} | wc -l) - 1));
+
+b_size=1
+
+echo "number of GALAXY_SLOTS: ${1}"
+
+echo "expected simulations: ${sim_number}"
+echo "cvle block size : ${b_size}"
+
+cvle -b $b_size -i ${2} -w work -P Stics4AgFlow -P CarSolEl_sim CarSolEl.vpz
+
+ls work_*/*_byUsm.txt | xargs -t -i tail -n +2 {} | sort -n -k 1 -t ';' > resWithoutHeader.csv
+
+head -1 work_0/1_byUsm.txt > header.cvs
+
+cat header.cvs resWithoutHeader.csv > res.csv
+
+mv res.csv ${3}
+
+echo "Stics4AgGlob Job ending:"
+date;
diff -r 000000000000 -r f1070dc2446c stics4carsolel.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stics4carsolel.xml	Mon Oct 25 11:32:31 2021 +0000
@@ -0,0 +1,37 @@
+<tool id="Stics4CarSolEl" name="Stics4CarSolEl" version="1.0.0">
+  <description>Vle Stics simulations in rotation parallelized by cvle for the CarSolEl project</description>
+  <requirements>
+    <container type="singularity">docker://registry.forgemia.inra.fr/record/carsolel</container>
+  </requirements>
+  <command detect_errors="exit_code">
+    bash $__tool_directory__/stics4carsolel.bash \${GALAXY_SLOTS:-2} ${cvle_plan} ${output_file};
+  </command>
+<inputs>
+  <param name="cvle_plan" type="data" format="csv" label="Select a cvle plan in (csv file)"/>
+</inputs>
+<outputs>
+  <data format='csv' name="output_file" label="Stics simulations results"/>
+</outputs>
+<tests>
+  <test>
+    <param name="cvle_plan" value="inputs/dummy50.csv" ftype="csv" />
+    <output name="output_file" ftype="csv">
+      <assert_contents>
+        <has_n_lines n="151" />
+      </assert_contents>
+    </output>
+  </test>
+</tests>
+<help>
+the Stics4CarSolEl simulator
+============================
+
+credits
+-------
+
+-  Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
+-  Tool Maintainer: Eric Casellas eric.casellas@inrae.fr
+-  Tool Site: https://forgemia.inra.fr/record/carsolel
+-  Copyright: INRAE
+</help>
+</tool>
diff -r 000000000000 -r f1070dc2446c test-data/inputs/dummy50.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputs/dummy50.csv	Mon Oct 25 11:32:31 2021 +0000
@@ -0,0 +1,51 @@
+cond_stics.SticsId,cond_stics.RecupFilePath,,,,,,,,,,,,,,
+1,./recup1,,,,,,,,,,,,,,
+2,./recup2,,,,,,,,,,,,,,
+3,./recup3,,,,,,,,,,,,,,
+4,./recup4,,,,,,,,,,,,,,
+5,./recup5,,,,,,,,,,,,,,
+6,./recup6,,,,,,,,,,,,,,
+7,./recup7,,,,,,,,,,,,,,
+8,./recup8,,,,,,,,,,,,,,
+9,./recup9,,,,,,,,,,,,,,
+10,./recup10,,,,,,,,,,,,,,
+11,./recup11,,,,,,,,,,,,,,
+12,./recup12,,,,,,,,,,,,,,
+13,./recup13,,,,,,,,,,,,,,
+14,./recup14,,,,,,,,,,,,,,
+15,./recup15,,,,,,,,,,,,,,
+16,./recup16,,,,,,,,,,,,,,
+17,./recup17,,,,,,,,,,,,,,
+18,./recup18,,,,,,,,,,,,,,
+19,./recup19,,,,,,,,,,,,,,
+20,./recup20,,,,,,,,,,,,,,
+21,./recup21,,,,,,,,,,,,,,
+22,./recup22,,,,,,,,,,,,,,
+23,./recup23,,,,,,,,,,,,,,
+24,./recup24,,,,,,,,,,,,,,
+25,./recup25,,,,,,,,,,,,,,
+26,./recup26,,,,,,,,,,,,,,
+27,./recup27,,,,,,,,,,,,,,
+28,./recup28,,,,,,,,,,,,,,
+29,./recup29,,,,,,,,,,,,,,
+30,./recup30,,,,,,,,,,,,,,
+31,./recup31,,,,,,,,,,,,,,
+32,./recup32,,,,,,,,,,,,,,
+33,./recup33,,,,,,,,,,,,,,
+34,./recup34,,,,,,,,,,,,,,
+35,./recup35,,,,,,,,,,,,,,
+36,./recup36,,,,,,,,,,,,,,
+37,./recup37,,,,,,,,,,,,,,
+38,./recup38,,,,,,,,,,,,,,
+39,./recup39,,,,,,,,,,,,,,
+40,./recup40,,,,,,,,,,,,,,
+41,./recup41,,,,,,,,,,,,,,
+42,./recup42,,,,,,,,,,,,,,
+43,./recup43,,,,,,,,,,,,,,
+44,./recup44,,,,,,,,,,,,,,
+45,./recup45,,,,,,,,,,,,,,
+46,./recup46,,,,,,,,,,,,,,
+47,./recup47,,,,,,,,,,,,,,
+48,./recup48,,,,,,,,,,,,,,
+49,./recup49,,,,,,,,,,,,,,
+50,./recup50,,,,,,,,,,,,,,