annotate neo4jsbml.xml @ 6:f2ababe65b04 draft

planemo upload for repository https://github.com/brsynth/neo4jsbml commit 537d7fefe58984b8f7ca66010153a2fdc35ddf4b

<tool id="neo4jsbml" name="neo4jsbml" version="@TOOL_VERSION@" profile="21.09" license="MIT">
    <description>Import SBML file into Neo4j</description>
    <macros>
        <token name="@TOOL_VERSION@">0.12.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">neo4jsbml</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python -m neo4jsbml
            --input-auradb-file '$input_auradb_file'
            --input-file-sbml '$input_file_sbml'
            #if str($input_tag_str) != ""
                --input-tag-str '$input_tag_str'
            #end if
            --input-modelisation-json '$input_modelisation_json' | tee '$output'
    ]]></command>
    <inputs>
        <param name="input_auradb_file" type="data" format="txt" label="Config file provided by AuraDB"/>
        <param name="input_file_sbml" type="data" format="sbml" label="SBML model"/>
        <param name="input_tag_str" type="text" label="Identifier of the model">
            <validator type="regex" message="No special characters allowed">^(?:[\w-]*)$</validator>
        </param>
        <param name="input_modelisation_json" type="data" format="json" label="Arrow's schema"/>
    </inputs>
    <outputs>
        <data name="output" format="txt" label="${tool.name} - log" />
    </outputs>
    <help><![CDATA[
Neo4jSbml
=========

Step 1
------

Create a schema with `Arrows <https://arrows.app>`_

Rules:
- Nodes are labelled based on SBML object name as defined in the `SBML specification <https://sbml.org>`_
- Properties are labelled based on SBML object properties as defined the `SBML specification <https://sbml.org>`_

Step 2
------
Export your schema at the JSON format.

Step 3
------

Import your data with `neo4jsbml` into Neo4j.
- Use either a configuration file `ini` or individual parameters
- Password needs to be store in a file for safety security
- 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

Inputs
------

- **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
- **SBML model**: SBML model
- **Identifier of the model**: Associate an ID to the nodes (optional)
- **Arrow's schema**: Schema created with Arrow

Ouput
-----

- Traceback of the tool
]]></help>
    <citations>
        <citation type="bibtex">
            @unpublished{neo4jsbml
                author = {Guillaume Gricourt, Thomas Duigou, Sandra Dérozier, Jean-Loup Faulon},
                title = {{Neo4jSbml}},
                url = {https://github.com/brsynth/neo4jsbml/},
            }
        </citation>
    </citations>
</tool>