Mercurial > repos > tduigou > neo4jsbml
changeset 3:7f1f5eedfbfc draft default tip
planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
| author | tduigou |
|---|---|
| date | Fri, 29 Sep 2023 11:37:37 +0000 |
| parents | eea256ad4d7f |
| children | |
| files | images/PathwayModelisation-1.0.0.arrows.png images/arrows.dwl.png neo4jsbml.xml |
| diffstat | 3 files changed, 16 insertions(+), 23 deletions(-) [+] |
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--- a/neo4jsbml.xml Fri Sep 29 11:22:10 2023 +0000 +++ b/neo4jsbml.xml Fri Sep 29 11:37:37 2023 +0000 @@ -59,51 +59,44 @@ Step 1 ------ -Create a schema with [arrows](https://arrows.app), following these rules: -.. image:: ${static_path}/images/PathwayModelisation-1.0.0.arrows.png - :width: 90 % - :align: center +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>`_ +- 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. -.. image:: ${static_path}/images/arrows.dwl.png - :width: 90 % - :align: center 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 - +- 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 +- **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 +- **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 +- Traceback of the tool ]]></help> <citations> <citation type="bibtex">