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changeset 3:e3153cc69e41 draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 67d85c013c62c16392b4796af86836b1334f2eef-dirty
author siwaa
date Fri, 07 Jun 2024 11:20:24 +0000
parents d203e560a4ef
children ee865d0f5132
files ESSAISENCOURS.txt gama_tool.xml src/:wq
diffstat 3 files changed, 127 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ESSAISENCOURS.txt	Fri Jun 07 11:20:24 2024 +0000
@@ -0,0 +1,37 @@
+#------------------------------------------------------------------------------
+# Done
+
+<tool id="gama_tool" name="gama" version="1.0.0b">
+
+8000 -> 6868
+
+=> tourne infini
+
+Note : consigne DOC image docker gama-server :
+docker run -v <path/to/your/workspace>:/working_dir -p 6868:6868 gamaplatform/gama:<version> -socket 6868
+NOUS, pas : -p 6868:6868 -socket 6868 !!!
+
+#------------------------------------------------------------------------------
+# Essai
+
+o
+  <command detect_errors="aggressive">
+    <![CDATA[
+    cp -fr /opt/gama-platform .;
+    cp $__tool_directory__/src/MY_predatorPrey.gaml gama-platform/headless/samples/predatorPrey/.;
+    cp $__tool_directory__/src/MY_gama-headless.sh gama-platform/headless/.;
+    cp $__tool_directory__/src/MY_sequential_example.py .;
+    cp $__tool_directory__/src/cmd_gama_headless.sh .;
+    cp $__tool_directory__/src/cmd_python_client.sh .;
+    /bin/bash cmd_gama_headless.sh > run_server.txt & sleep 120 && /bin/bash cmd_python_client.sh $nb_preys_init $nb_predators_init $nb_more_steps > run_client.txt;
+    cp run_server.txt ${run_server_txt};
+    cp run_client.txt ${run_client_txt};
+    cp gama-platform/headless/samples/predatorPrey/results.txt ${results_txt};
+    ]]>
+  </command>
+
+
+
+
+#------------------------------------------------------------------------------
+
--- a/gama_tool.xml	Fri Jun 07 10:52:37 2024 +0000
+++ b/gama_tool.xml	Fri Jun 07 11:20:24 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="gama_tool" name="gama" version="1.0.0a">
+<tool id="gama_tool" name="gama" version="1.0.0b">
 
   <description>tool for GAMA Platform</description>
 
@@ -19,7 +19,7 @@
     cp $__tool_directory__/src/MY_sequential_example.py .;
     cp $__tool_directory__/src/cmd_gama_headless.sh .;
     cp $__tool_directory__/src/cmd_python_client.sh .;
-    /bin/bash cmd_gama_headless.sh > run_server.txt & sleep 20 && /bin/bash cmd_python_client.sh $nb_preys_init $nb_predators_init $nb_more_steps > run_client.txt;
+    /bin/bash cmd_gama_headless.sh > run_server.txt & sleep 120 && /bin/bash cmd_python_client.sh $nb_preys_init $nb_predators_init $nb_more_steps > run_client.txt;
     cp run_server.txt ${run_server_txt};
     cp run_client.txt ${run_client_txt};
     cp gama-platform/headless/samples/predatorPrey/results.txt ${results_txt};
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/:wq	Fri Jun 07 11:20:24 2024 +0000
@@ -0,0 +1,88 @@
+<tool id="gama_tool" name="gama" version="1.0.0b">
+
+  <description>tool for GAMA Platform</description>
+
+  <requirements>
+
+    <!-- singularity -->
+    <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/gama:d01c3645810b3e5bf1b21170fd24d21fe1f831ec</container>
+
+    <!-- image locale 
+    <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_gama/use/GAMA/containers/gama.simg</container -->
+  </requirements>
+
+  <command detect_errors="aggressive">
+    <![CDATA[
+    cp -fr /opt/gama-platform .;
+    cp $__tool_directory__/src/MY_predatorPrey.gaml gama-platform/headless/samples/predatorPrey/.;
+    cp $__tool_directory__/src/MY_gama-headless.sh gama-platform/headless/.;
+    cp $__tool_directory__/src/MY_sequential_example.py .;
+    cp $__tool_directory__/src/cmd_gama_headless.sh .;
+    cp $__tool_directory__/src/cmd_python_client.sh .;
+    /bin/bash cmd_gama_headless.sh > run_server.txt & sleep 120 && /bin/bash cmd_python_client.sh $nb_preys_init $nb_predators_init $nb_more_steps > run_client.txt;
+    cp run_server.txt ${run_server_txt};
+    cp run_client.txt ${run_client_txt};
+    cp gama-platform/headless/samples/predatorPrey/results.txt ${results_txt};
+    ]]>
+  </command>
+
+  <inputs>
+
+    <param name="nb_preys_init" optional="true" type="integer"
+           value="200" min="0" max="1000"
+           label="nb_preys_init" help="[0, 1000]" />
+
+    <param name="nb_predators_init" optional="true" type="integer"
+           value="20" min="0" max="200"
+           label="nb_predators_init" help="[0, 200]" />
+
+    <param name="nb_more_steps" optional="true" type="integer"
+           value="10" min="4" max="100"
+           label="nb_more_steps" help="[4,100]" />
+
+  </inputs>
+
+  <outputs>
+    <data format="txt" name="run_server_txt" label="run_server_txt"/>
+    <data format="txt" name="run_client_txt" label="run_client_txt"/>
+    <data format="txt" name="results_txt" label="results_txt"/>
+  </outputs>
+
+  <tests>
+  </tests>
+
+  <help><![CDATA[
+
+Desc:
+
+-----
+
+gama_tool.xml tool running a GAMA Python client interacting with gama-server
+(Headless server) concerning a "Predator Prey" agent-based simulator.
+
+Code: MY_sequential_example.py
+
+Inputs:
+
+  - nb_preys_init
+  - nb_predators_init
+  - nb_more_steps
+
+Outputs:
+
+  - results_txt file (.txt) : produced while running the simulator
+    (cf 'reflex save_result' into MY_predatorPrey.gaml).
+  - run_server_txt file (.txt) : gama-server screen display capture
+  - run_client_txt file (.txt) : gama-client screen display capture
+
+Credits:
+
+--------
+
+-  Author: Nathalie Rousse nathalie.rousse@inrae.fr
+-  Copyright: INRAE
+
+  ]]>
+  </help>
+
+</tool>