Mercurial > repos > siwaa > erecord_json

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 490623122691651ac91c33d75ea1898189be7512-dirty
author siwaa
date Thu, 15 Feb 2024 15:24:41 +0000
parents afc88ac8de69
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8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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1 <tool id="erecord_json" name="erecord_json" version="1.0.0">
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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3 <description>erecord returning .json</description>
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5 <requirements>
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7 <!-- singularity -->
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afc88ac8de69 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
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8 <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/erecord-deploy/rep_recordb:9d6ea1defd50dd63fe036a7545a9ea527572192e</container>
afc88ac8de69 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
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afc88ac8de69 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
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10 <!-- image locale -->
afc88ac8de69 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
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11 <!-- container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/erecord-deploy/containers/_fab_SIMG/rep_recordb.simg</container-->
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8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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13 </requirements>
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15 <command detect_errors="aggressive">
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16 <![CDATA[
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17 . /PYVENV/bin/activate;
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18 /bin/bash -c "python3 $__tool_directory__/main_json.py -data ${input_json} -datafolder ${datafolder}";
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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19 cp WS/OUT/output.json ${output_json};
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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20 ]]>
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21 </command>
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23 <inputs>
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25 <param name="input_json" optional="true" type="data" format="json"
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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26 label="Input json file"/>
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28 <param name="datafolder" optional="true" type="data" format="zip"
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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29 label="Add a datafolder zip file (available and used only in 'post_vpz_output' or 'post_vpz_inout' cases)"
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30 help="Precisions sur forme du dossier..."/>
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32 </inputs>
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34 <outputs>
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35 <data format="json" name="output_json" label="jsonoutput"/>
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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36 </outputs>
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38 <tests>
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39 </tests>
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41 <help><![CDATA[
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43 erecord_json.xml
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45 ================
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47 Actions:
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49 -------
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8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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51 - Available :
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52 - 'get_vpz_input' 'post_vpz_input'
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53 - 'get_vpz_output' 'post_vpz_output'
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54 - 'get_vpz_inout' 'post_vpz_inout'
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55 - 'get_pkg_list' 'get_pkg_vpz_list' 'get_pkg_data_list'
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56 - 'help'
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57
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58 - Unavailable (actions with 2 output files) :
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59 - 'get_vpz_experiment' 'post_vpz_experiment'
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60 - 'get_vpz_report_conditions' 'post_vpz_report_conditions'
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61 - 'get_vpz_report' 'post_vpz_report'
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63 Code:
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65 ----
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8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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67 - main_json.py
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69 Inputs:
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71 -------
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73 - data json file (optional) (json file, param type="data")
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75 This file contains the action value
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77 - datafolder (optional) (only in 'post_vpz_output', 'post_vpz_inout' cases)
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8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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79 Outputs:
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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80
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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81 --------
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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82
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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83 - data json file (no other file returned)
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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84
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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85 Credits:
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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86
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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87 --------
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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88
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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89 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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90 - Copyright: INRAE
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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91
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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92 ]]>
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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93 </help>
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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94
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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95 </tool>