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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 14769577c04bcb2781b2d240f1f57a2342169cce-dirty
author siwaa
date Fri, 02 Aug 2024 18:02:56 +0000
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1 <tool id="gama_legacy_gen" name="gama_legacy_gen" version="1.0.0">
2
3 <description>tool generating XML file from 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 inputs; mkdir -p outputs;
17 cp $__tool_directory__/src/MY_gama-headless.sh .;
18 cp $__tool_directory__/src/cmd_gama_headless_legacy_gen.sh .;
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;
23 /bin/bash cmd_gama_headless_legacy_gen.sh ${experiment_name} > outputs/GEN.txt;
24 xmlstarlet edit --inplace --update "//Simulation/@sourcePath" --value "model.gaml" outputs/file.xml;
25 cp outputs/file.xml ${file_xml};
26 ]]>
27 </command>
28
29 <inputs>
30
31 <param name="experiment_name" optional="false" type="text"
32 value="prey_predator"
33 label="experiment_name"
34 help="name of an experiment that must exist into gaml file as 'experiment' of type': 'gui'" />
35
36 <param name="model_gaml" optional="false" type="data" format="txt"
37 label="GAML model (.gaml format)"/>
38
39 </inputs>
40
41 <outputs>
42 <data format="xml" name="file_xml" label="XML file of experiment plan"/>
43 </outputs>
44
45 <tests>
46 </tests>
47
48 <help><![CDATA[
49
50 Desc:
51
52 -----
53
54 gama_legacy_gen.xml tool, running a GAMA Headless in 'Legacy' mode, generates
55 the XML file 'file_xml' corresponding with the experiment 'experiment_name'
56 (of 'type': 'gui') contained into the GAML file 'model_gaml'.
57
58 Inputs:
59
60 - experiment_name
61 - model_gaml
62
63 Outputs:
64
65 - file_xml
66
67 Credits:
68
69 --------
70
71 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
72 - Copyright: INRAE
73
74 ]]>
75 </help>
76
77 </tool>
78