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comparison gama_legacy_run.xml @ 0:986f43279bca draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_run commit 14769577c04bcb2781b2d240f1f57a2342169cce-dirty
author siwaa
date Fri, 02 Aug 2024 18:03:16 +0000
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-1:000000000000 0:986f43279bca
1 <tool id="gama_legacy_run" name="gama_legacy_run" version="1.0.0">
2
3 <description>tool running an experiment plan XML file associated with a GAML file (GAMA Headless Legacy mode)</description>
4
5 <requirements>
6
7 <!-- singularity -->
8 <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/gama_headless:e45168638437055475beeaa614611cb315a56fca</container>
9
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 -->
12 </requirements>
13
14 <command detect_errors="aggressive">
15 <![CDATA[
16 mkdir -p software; mkdir -p exp;
17 cp $__tool_directory__/src/MY_gama-headless.sh .;
18 cp $__tool_directory__/src/cmd_gama_headless_legacy_run.sh .;
19 cp ${model_gaml} exp/model.gaml;
20 cp ${file_xml} exp/file.xml;
21 xmlstarlet edit --inplace --update "//Simulation/@sourcePath" --value "model.gaml" exp/file.xml;
22 xmlstarlet edit --inplace --update "//Simulation/@finalStep" --value "${final_step}" exp/file.xml;
23 cp -fr /opt/gama-platform software/.;
24 cp MY_gama-headless.sh software/gama-platform/headless/. ;
25 chmod -R 777 software;
26 /bin/bash cmd_gama_headless_legacy_run.sh > exp/RUN.txt;
27 rm -fr exp/outputs/.workspace*;
28 zip -r tmp_result exp;
29 mv tmp_result.zip ${result_zip};
30 ]]>
31 </command>
32
33 <inputs>
34
35 <param name="file_xml" optional="false" type="data" format="xml"
36 label="XML file of experiment plan (.xml format)"/>
37
38 <param name="model_gaml" optional="false" type="data" format="txt"
39 label="GAML model (.gaml format)"/>
40
41 <param name="final_step" optional="true" type="integer"
42 value="1000" min="10" max="2000"
43 label="final_step"
44 help="'finalStep' attribute of 'experiment' tag [10, 2000]" />
45
46 </inputs>
47
48 <outputs>
49 <data format="zip" name="result_zip" label=".zip file of results folder"/>
50 </outputs>
51
52 <tests>
53 </tests>
54
55 <help><![CDATA[
56
57 Desc:
58
59 -----
60
61 gama_legacy_run.xml tool, running a GAMA Headless in 'Legacy' mode, runs
62 an experiment plan XML file 'file_xml' (such as XML file generated by
63 gama_legacy_gen.xml tool) associated with its GAML file 'model_gaml',
64 allowing some modifications of the plan : 'final_step' modification.
65
66 Inputs:
67
68 - file_xml
69 - model_gaml
70 - final_step
71
72 Outputs:
73
74 - result_zip
75
76 Credits:
77
78 --------
79
80 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
81 - Copyright: INRAE
82
83 ]]>
84 </help>
85
86 </tool>
87