<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@">1.0.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">neo4jsbml</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        neo4jsbml sbml-to-neo4j
            --input-auradb-txt '$input_auradb_txt'
            --input-file-sbml '$input_file_sbml'
            #if str($parameter_tag_property_str) != ""
                --parameter-tag-property-str '$parameter_tag_property_str'
            #end if
            --input-arrows-json '$input_arrows_json' | tee '$output'
    ]]></command>
    <inputs>
        <param name="input_auradb_txt" type="data" format="txt" label="Config file provided by AuraDB"/>
        <param name="input_file_sbml" type="data" format="sbml" label="SBML model"/>
        <param name="parameter_tag_property_str" type="text" label="Identifier of the model">
            <validator type="regex" message="No special characters allowed">^(?:[\w-]*)$</validator>
        </param>
        <param name="input_arrows_json" type="data" format="json" label="Arrow's schema"/>
    </inputs>
    <outputs>
        <data name="output" format="txt" label="${tool.name} - log" />
    </outputs>
    <tests>
        <test>
            <param name="input_file_sbml" value="e_coli_core.xml.gz" />
            <param name="input_arrows_json" value="PathwayModelisation-2.0.3.json" />
            <param name="input_auradb_txt" value="test_auradb.txt" />
            <param name="parameter_tag_property_str" value="parameter" />
            <output name="output" ftype="txt" >
                <assert_contents>
                    <has_size value="1000" delta="500" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <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">
            @article{gricourt_neo4jsbml_2024,
                title = {neo4jsbml: import systems biology markup language data into the graph database {Neo4j}},
                volume = {12},
                issn = {2167-8359},
                url = {https://peerj.com/articles/16726},
                doi = {10.7717/peerj.16726},
                urldate = {2024-01-22},
                journal = {PeerJ},
                author = {Gricourt, Guillaume and Duigou, Thomas and Dérozier, Sandra and Faulon, Jean-Loup},
                month = jan,
                year = {2024},
                pages = {e16726},
            }
        </citation>
    </citations>
</tool>