Mercurial > repos > siwaa > insilicow
comparison insilicow.xml @ 0:50112d3941d8 draft
"planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
| author | siwaa |
|---|---|
| date | Mon, 07 Apr 2025 15:18:25 +0000 |
| parents | |
| children | f2840b46b353 |
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| -1:000000000000 | 0:50112d3941d8 |
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| 1 <tool id="inSiliCow" name="inSiliCow" version="1.0.0"> | |
| 2 <description>to run the inSiliCow simulator</description> | |
| 3 <requirements> | |
| 4 <container type="singularity">docker://registry.forgemia.inra.fr/insilicow/insilicow-container:6d9cbffcf24d3af29b244ea3543c53b4298077de</container> | |
| 5 </requirements> | |
| 6 <command detect_errors="aggressive"> | |
| 7 <![CDATA[ | |
| 8 echo "=================" && | |
| 9 env && | |
| 10 echo "=================" && | |
| 11 cp -r /insilicow-simulator . && | |
| 12 cd insilicow-simulator/scripts && | |
| 13 cp $__tool_directory__/inSiliCow-run.sh . && | |
| 14 cp $__tool_directory__/inSiliCow-post.sh . && | |
| 15 rm -rf examples/e* && | |
| 16 unzip -d tmp ${in} && | |
| 17 configDir=\$(ls -1 tmp) && | |
| 18 mv tmp/* examples && | |
| 19 pwd && ls && echo \$configDir && | |
| 20 chmod u+x ./inSiliCow-run.sh && | |
| 21 TERM="xterm-256color" ./inSiliCow-run.sh \$configDir && | |
| 22 cd out && | |
| 23 zip -r j* * && | |
| 24 mv *.zip ${out} | |
| 25 ]]> | |
| 26 </command> | |
| 27 <inputs> | |
| 28 <param name="in" type="data" format="zip" label="Select a inSiliCow config folder (zip file)"/> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data format="zip" name="out" | |
| 32 label="inSiliCowOutputs"> | |
| 33 </data> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="in" value="input/example_00.zip" ftype="zip" /> | |
| 38 <output name="out" ftype="zip" > | |
| 39 <assert_contents> | |
| 40 <has_archive_member path=".*/out/farmer.sh"> | |
| 41 <has_size value="0" negate="true" /> | |
| 42 </has_archive_member> | |
| 43 <has_archive_member path=".*/in/explan.txt"> | |
| 44 <has_size value="0" negate="true" /> | |
| 45 <has_text text="end_year" /> | |
| 46 <has_text text="1971" /> | |
| 47 </has_archive_member> | |
| 48 <has_archive_member path=".*/out/sim_1/events.sqlite"> | |
| 49 <has_size value="0" negate="true" /> | |
| 50 </has_archive_member> | |
| 51 <has_archive_member path=".*/out/sim_1/states.txt"> | |
| 52 <has_size value="0" negate="true" /> | |
| 53 <has_text text="CALF" /> | |
| 54 </has_archive_member> | |
| 55 <has_archive_member path=".*/out/sim_1/cows/nb_cows.txt"> | |
| 56 <has_text text="126" /> | |
| 57 </has_archive_member> | |
| 58 </assert_contents> | |
| 59 </output> | |
| 60 </test> | |
| 61 </tests> | |
| 62 <help> | |
| 63 *The usage of this tool is restricted to the user of the redelac_authorized group.* | |
| 64 | |
| 65 *To be granted, apply to the REDELAC Project Team and then request to SIWAA* | |
| 66 | |
| 67 Documentation | |
| 68 ------------- | |
| 69 A tool to generate Stics Inputs according to a plan for REDELAC | |
| 70 | |
| 71 Credits | |
| 72 ------- | |
| 73 - Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team | |
| 74 - Stics Site: https://www6.paca.inra.fr/stics_eng | |
| 75 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr | |
| 76 - Copyright: INRAE | |
| 77 </help> | |
| 78 </tool> |