Mercurial > repos > siwaa > erecord_json

annotate erecord_json.xml @ 1:d87b8a1073ad draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit ac10d874b1abe19a8c44f861b2f180ff20976b39
author siwaa
date Wed, 13 Dec 2023 21:46:11 +0000
parents 8a0659f23df7
children 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>
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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5 <requirements>
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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7 <!-- singularity -->
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d87b8a1073ad planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit ac10d874b1abe19a8c44f861b2f180ff20976b39
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8 <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/erecord-deploy/erecord_rep0_vle2:53e4840cd66e45761db955f69203284761fd6df8</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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10 </requirements>
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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12 <command detect_errors="aggressive">
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 <![CDATA[
1
d87b8a1073ad planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit ac10d874b1abe19a8c44f861b2f180ff20976b39
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14 . /PYVENV/bin/activate;
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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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15 /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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16 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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17 ]]>
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18 </command>
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 <inputs>
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22 <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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23 label="Input json file"/>
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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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25 <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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26 label="Add a datafolder zip file (available and used only in 'post_vpz_output' or 'post_vpz_inout' cases)"
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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27 help="Precisions sur forme du dossier..."/>
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 </inputs>
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31 <outputs>
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32 <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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33 </outputs>
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35 <tests>
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36 </tests>
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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38 <help><![CDATA[
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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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40 erecord_json.xml
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42 ================
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44 Actions:
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46 -------
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48 - Available :
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49 - 'get_vpz_input' 'post_vpz_input'
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50 - 'get_vpz_output' 'post_vpz_output'
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51 - 'get_vpz_inout' 'post_vpz_inout'
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52 - 'get_pkg_list' 'get_pkg_vpz_list' 'get_pkg_data_list'
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53 - 'help'
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55 - Unavailable (actions with 2 output files) :
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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56 - 'get_vpz_experiment' 'post_vpz_experiment'
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57 - 'get_vpz_report_conditions' 'post_vpz_report_conditions'
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58 - 'get_vpz_report' 'post_vpz_report'
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60 Code:
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62 ----
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64 - main_json.py
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66 Inputs:
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68 -------
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70 - data json file (optional) (json file, param type="data")
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72 This file contains the action value
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74 - datafolder (optional) (only in 'post_vpz_output', 'post_vpz_inout' cases)
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76 Outputs:
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78 --------
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79
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 - 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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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 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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83
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
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 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
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87 - 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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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 ]]>
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 </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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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 </tool>