comparison neo4jsbml.xml @ 5:6941e7dc5117 draft

planemo upload for repository https://github.com/brsynth/neo4jsbml commit 8dd843aac9f23dd9e0036c48914f20889d894ecc

4:94863d48d5da

            --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_log'
    ]]></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-]*)$</validator>
        </param>
        <param name="input_modelisation_json" type="data" format="json" label="Arrow's schema"/>
    </inputs>
    <outputs>
        <data name="output_log" format="txt" label="${tool.name} - log" />
    </outputs>
    <help><![CDATA[
Neo4jSbml
=========

- 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
-----

5:6941e7dc5117

            --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
=========

- 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
-----