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annotate neo4jsbml.xml @ 8:dd3b699966da draft default tip

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planemo upload for repository https://github.com/brsynth/neo4jsbml commit e8c8f102cab10531ed588be4ecb8a0d01e797f09
author tduigou
date Tue, 06 Jan 2026 11:38:05 +0000
parents f76091ce926e
children
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1 <tool id="neo4jsbml" name="neo4jsbml" version="@TOOL_VERSION@" profile="21.09" license="MIT">
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2 <description>Import SBML file into Neo4j</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.0.1</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">neo4jsbml</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 neo4jsbml sbml-to-neo4j
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11 --input-auradb-txt '$input_auradb_txt'
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12 --input-file-sbml '$input_file_sbml'
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13 #if str($parameter_tag_property_str) != ""
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14 --parameter-tag-property-str '$parameter_tag_property_str'
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15 #end if
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16 --input-arrows-json '$input_arrows_json' | tee '$output'
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17 ]]></command>
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18 <inputs>
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19 <param name="input_auradb_txt" type="data" format="txt" label="Config file provided by AuraDB"/>
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20 <param name="input_file_sbml" type="data" format="sbml" label="SBML model"/>
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21 <param name="parameter_tag_property_str" type="text" label="Identifier of the model">
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22 <validator type="regex" message="No special characters allowed">^(?:[\w-]*)$</validator>
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23 </param>
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24 <param name="input_arrows_json" type="data" format="json" label="Arrow's schema"/>
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25 </inputs>
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26 <outputs>
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27 <data name="output" format="txt" label="${tool.name} - log" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input_file_sbml" value="e_coli_core.xml.gz" />
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32 <param name="input_arrows_json" value="PathwayModelisation-2.0.3.json" />
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33 <param name="input_auradb_txt" value="test_auradb.txt" />
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34 <param name="parameter_tag_property_str" value="parameter" />
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35 <output name="output" ftype="txt" >
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36 <assert_contents>
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37 <has_size value="1000" delta="500" />
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38 </assert_contents>
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39 </output>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 Neo4jSbml
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44 =========
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46 Step 1
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47 ------
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49 Create a schema with `Arrows <https://arrows.app>`_
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51 Rules:
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52 - Nodes are labelled based on SBML object name as defined in the `SBML specification <https://sbml.org>`_
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53 - Properties are labelled based on SBML object properties as defined the `SBML specification <https://sbml.org>`_
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54
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55 Step 2
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56 ------
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57 Export your schema at the JSON format.
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58
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59 Step 3
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60 ------
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61
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62 Import your data with `neo4jsbml` into Neo4j.
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63 - Use either a configuration file `ini` or individual parameters
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64 - Password needs to be store in a file for safety security
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65 - If you have multiple model in the database, pass a `tag` to identify the model loaded into the database if you want to avoid collision
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66
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67 Inputs
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68 ------
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69
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70 - **AuraDB config like**: a txt file with these variables NEO4J_URI, NEO4J_USERNAME, NEO4J_PASSWORD and AURA_INSTANCENAME. One per line like: NEO4J_USERNAME=neo4j
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71 - **SBML model**: SBML model
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72 - **Identifier of the model**: Associate an ID to the nodes (optional)
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73 - **Arrow's schema**: Schema created with Arrow
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74
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75 Ouput
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76 -----
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77
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78 - Traceback of the tool
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79 ]]></help>
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80 <citations>
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81 <citation type="bibtex">
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82 @article{gricourt_neo4jsbml_2024,
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83 title = {neo4jsbml: import systems biology markup language data into the graph database {Neo4j}},
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84 volume = {12},
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85 issn = {2167-8359},
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86 url = {https://peerj.com/articles/16726},
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87 doi = {10.7717/peerj.16726},
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88 urldate = {2024-01-22},
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89 journal = {PeerJ},
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90 author = {Gricourt, Guillaume and Duigou, Thomas and Dérozier, Sandra and Faulon, Jean-Loup},
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91 month = jan,
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92 year = {2024},
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93 pages = {e16726},
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94 }
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95 </citation>
748d0a0925cb planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
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parents:
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96 </citations>
748d0a0925cb planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
tduigou
parents:
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97 </tool>