Mercurial > repos > siwaa > erecord_text

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_text commit c9272a57d834895bf21c987be7d7416532cfa23f-dirty
author siwaa
date Tue, 27 Feb 2024 07:58:55 +0000
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5edb952b394e planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_text commit c9272a57d834895bf21c987be7d7416532cfa23f-dirty
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1 <tool id="erecord_text" name="erecord_text" version="1.0.0">
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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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8 <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/erecord-deploy/rep_recordb:9d6ea1defd50dd63fe036a7545a9ea527572192e</container>
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10 <!-- image locale -->
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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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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 $__tool_directory__/main_text.py -data '${input_text}' -datafolder ${datafolder}";
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19 cp WS/OUT/output.json ${output_json};
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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_text" optional="true" type="text" area="true"
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26 label="Input json as text"/>
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28 <param name="datafolder" optional="true" type="data" format="zip"
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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"/>
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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_text.xml
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45 ================
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47 Actions:
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49 -------
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51 - Available :
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53 - 'get_vpz_input' 'post_vpz_input'
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54 - 'get_vpz_output' 'post_vpz_output'
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55 - 'get_vpz_inout' 'post_vpz_inout'
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56 - 'get_pkg_list' 'get_pkg_vpz_list' 'get_pkg_data_list'
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57 - 'help'
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59 - Unavailable (actions with 2 output files) :
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61 - 'get_vpz_experiment' 'post_vpz_experiment'
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62 - 'get_vpz_report_conditions' 'post_vpz_report_conditions'
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63 - 'get_vpz_report' 'post_vpz_report'
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65 Code:
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67 ----
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69 - main_text.py
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71 Inputs:
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73 -------
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75 - data json as text (optional) (text, param type="text")
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77 - This data contains the action value
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78 - Examples :
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80 - {"action":"pkg_list"}
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81 - {"action": "post_vpz_output", "pkgname": "wwdm", "vpzname": "wwdm.vpz", "style": "compactlist", "plan":"linear", "restype" : "matrix", "cond_wwdm.A": [0.0063, 0.0065, 0.0067], "cond_wwdm.B": 0.00201, "duration":6.0, "outselect": "view"}
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82
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83 - datafolder (optional) (only in 'post_vpz_output', 'post_vpz_inout' cases)
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84
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85 Outputs:
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86
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87 --------
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89 - data json file (no other file returned)
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90
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91 Credits:
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92
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93 --------
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95 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
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96 - Copyright: INRAE
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97
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98 ]]>
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99 </help>
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100
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101 </tool>