comparison neo4jsbml.xml @ 7:f76091ce926e draft default tip

planemo upload for repository https://github.com/brsynth/neo4jsbml commit 96a30e92eab3144b924fdba7b63be10b218160a7

6:f2ababe65b04

<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[

- 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            @unpublished{neo4jsbml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>

7:f76091ce926e

<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>
    <help><![CDATA[

- 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>