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comparison gama_legacy_gen.xml @ 11:770e0dde4735 draft default tip

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 8731d8cb947d6b7b65eb0fde51a4b0f44c2f4406-dirty
author siwaa
date Fri, 20 Dec 2024 23:16:10 +0000
parents f57ea38d67c5
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10:f57ea38d67c5 11:770e0dde4735
3 <description>tool generating XML file from GAML file</description> 3 <description>tool generating XML file from GAML file</description>
4 4
5 <requirements> 5 <requirements>
6 6
7 <!-- singularity --> 7 <!-- singularity -->
8 <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/gama_headless:74ad70560393b1198b7f329fa4f1355643cc2250</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/gama_headless:0356ba7eb250433405698597a802d8a6b4e04967</container>
9 9
10 <!-- image locale 10 <!-- image locale
11 <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_gama/use/GAMA_HEADLESS_LEGACY/containers/gama_headless.simg</container --> 11 <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_gama/use/GAMA_HEADLESS_LEGACY/containers/gama_headless.simg</container -->
12 </requirements> 12 </requirements>
13 13
14 <command detect_errors="aggressive"> 14 <command detect_errors="aggressive">
15 <![CDATA[ 15 <![CDATA[
16 mkdir -p inputs; mkdir -p outputs; 16 mkdir -p software; mkdir -p inputs; mkdir -p outputs;
17 cp $__tool_directory__/src/MY_gama-headless.sh .;
17 cp $__tool_directory__/src/cmd_gama_headless_legacy_gen.sh .; 18 cp $__tool_directory__/src/cmd_gama_headless_legacy_gen.sh .;
18 cp ${model_gaml} inputs/model.gaml; 19 cp ${model_gaml} inputs/model.gaml;
20 cp -fr /opt/gama-platform software/.;
21 cp MY_gama-headless.sh software/gama-platform/headless/. ;
22 chmod -R 777 software;
19 /bin/bash cmd_gama_headless_legacy_gen.sh ${experiment_name} > outputs/GEN.txt; 23 /bin/bash cmd_gama_headless_legacy_gen.sh ${experiment_name} > outputs/GEN.txt;
20 xmlstarlet edit --inplace --update "//Simulation/@sourcePath" --value "model.gaml" outputs/file.xml; 24 xmlstarlet edit --inplace --update "//Simulation/@sourcePath" --value "model.gaml" outputs/file.xml;
21 cp outputs/file.xml ${file_xml}; 25 cp outputs/file.xml ${file_xml};
22 ]]> 26 ]]>
23 </command> 27 </command>