--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/insilicow.xml	Mon Apr 07 15:18:25 2025 +0000
@@ -0,0 +1,78 @@
+<tool id="inSiliCow" name="inSiliCow" version="1.0.0">
+  <description>to run the inSiliCow simulator</description>
+  <requirements>
+    <container type="singularity">docker://registry.forgemia.inra.fr/insilicow/insilicow-container:6d9cbffcf24d3af29b244ea3543c53b4298077de</container>
+  </requirements>
+  <command detect_errors="aggressive">
+    <![CDATA[
+	     echo "=================" &&
+	     env &&
+	     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 &&
+	     pwd && ls && echo \$configDir &&
+	     chmod u+x ./inSiliCow-run.sh &&
+	     TERM="xterm-256color" ./inSiliCow-run.sh \$configDir &&
+	     cd out &&
+	     zip -r j* * &&
+	     mv *.zip ${out}
+     ]]>
+  </command>
+  <inputs>
+    <param name="in" type="data" format="zip" label="Select a inSiliCow config folder (zip file)"/>
+  </inputs>
+  <outputs>
+    <data format="zip" name="out"
+          label="inSiliCowOutputs">
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="in" value="input/example_00.zip" ftype="zip" />
+      <output name="out" ftype="zip" >
+	<assert_contents>
+	  <has_archive_member path=".*/out/farmer.sh">
+	    <has_size value="0" negate="true" />
+	  </has_archive_member>
+	  <has_archive_member path=".*/in/explan.txt">
+	    <has_size value="0" negate="true" />
+	    <has_text text="end_year" />
+	    <has_text text="1971" />
+	  </has_archive_member>
+	  <has_archive_member path=".*/out/sim_1/events.sqlite">
+	    <has_size value="0" negate="true" />
+	  </has_archive_member>
+	  <has_archive_member path=".*/out/sim_1/states.txt">
+	    <has_size value="0" negate="true" />
+	    <has_text text="CALF" />
+	  </has_archive_member>
+	  <has_archive_member path=".*/out/sim_1/cows/nb_cows.txt">
+	    <has_text text="126" />
+	  </has_archive_member>
+	</assert_contents>	  
+      </output>
+    </test>
+  </tests>
+  <help>
+*The usage of this tool is restricted to the user of the redelac_authorized group.*
+
+*To be granted, apply to the REDELAC Project Team and then request to SIWAA*
+
+Documentation
+-------------
+A tool to generate Stics Inputs according to a plan for REDELAC
+
+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>