<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@">0.11.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">neo4jsbml</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python -m neo4jsbml
            --input-protocol-str '$input_protocol_str'
            --input-url-str '$input_url_str'
            --input-port-int '$input_port_int'
            --input-user-str '$input_user_str'
            --input-password-file '$input_password_file'
            --input-database-str '$input_database_str'

            --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' > '$output_log'
    ]]></command>
    <inputs>
        <param name="input_protocol_str" type="select" label="Protocol">
            <option value="neo4j" selected="true">neo4j</option>
            <option value="neo4j+s">neo4j+s</option>
            <option value="neo4j+ssc">neo4j+ssc</option>
            <option value="bolt">bolt</option>
            <option value="bolt+s">bolt+s</option>
            <option value="bolt+ssc">bolt+ssc</option>
        </param>
        <param name="input_url_str" type="text" label="Url of the database">
            <validator type="empty_field" message="Not empty"/>
        </param>
        <param name="input_port_int" type="text" value="7687" label="Port of the database">
            <validator type="empty_field" message="Not empty"/>
            <validator type="regex" message="Only integers are allowed">^(?:\d+)$</validator>
        </param>
        <param name="input_user_str" type="text" value="neo4j" label="Username of the database">
            <validator type="empty_field" message="Not empty"/>
        </param>
        <param name="input_password_file" type="data" format="txt" label="Password of the database"/>
        <param name="input_database_str" type="text" label="Database name">
            <validator type="empty_field" message="Not empty"/>
        </param>

        <param name="input_file_sbml" type="data" format="sbml" label="SBML model"/>
        <param name="input_tag_str" type="text" label="Identifier of the model"/>
        <param name="input_modelisation_json" type="data" format="json" label="Arrow's schema"/>
    </inputs>
    <outputs>
        <data name="output_log" 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
------

Database parameters
- **Protocol**: choose the protocol (default: neo4j)
- **Url of the database**: define the url of the database
- **Port of the database**: define the port of the database (default: 7687)
- **Username of the database**: User name of the database
- **Password of the database**: file with the password
- **Database name**: database name

Input
- **SBML model**: SBML model
- **Identifier of the model**: Associate an ID to the nodes
- **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>