# HG changeset patch
# User siwaa
# Date 1748421442 0
# Node ID 2722892ff716bb08875ddc0981751a1c8749c4c9
# Parent  f2840b46b353f6bf146c91bb5ac9f87933295618
"planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit d91a7371e51377d199865ad1c6d5b70afbf2c414"

diff -r f2840b46b353 -r 2722892ff716 insilicow.xml
--- a/insilicow.xml	Thu Apr 10 15:22:42 2025 +0000
+++ b/insilicow.xml	Wed May 28 08:37:22 2025 +0000
@@ -1,7 +1,7 @@
-<tool id="inSiliCow" name="inSiliCow" version="1.0.1">
+<tool id="inSiliCow" name="inSiliCow" version="1.0.2">
   <description>to run the inSiliCow simulator</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/insilicow/insilicow-container:6d9cbffcf24d3af29b244ea3543c53b4298077de</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/insilicow/insilicow-container:ea8a24d5d56c3d12d53303db6d47ef77382c843f</container>
   </requirements>
   <command detect_errors="aggressive">
     <![CDATA[
@@ -10,13 +10,13 @@
 	     echo "=================" &&
 	     cp -r /insilicow-simulator . &&
 	     cd insilicow-simulator/scripts &&
-	     cp  $__tool_directory__/inSiliCow-run.sh . &&
-	     cp  $__tool_directory__/inSiliCow-post.sh . &&
-	     rm -rf examples/e* &&
 	     unzip -d tmp ${in} &&
 	     configDir=\$(ls -1 tmp) &&
-	     mv tmp/* examples &&
+	     find examples/* -type d | xargs rm -R &&
+	     mv -f tmp/* examples &&
 	     pwd && ls && echo \$configDir &&
+	     head -n -3 ./inSiliCow-run.sh > tmpFile &&
+	     mv tmpFile ./inSiliCow-run.sh &&
 	     chmod u+x ./inSiliCow-run.sh &&
 	     TERM="xterm-256color" ./inSiliCow-run.sh \$configDir &&
 	     cd out &&