comparison Marea/marea_macros.xml @ 1:9e63d5f02d62 draft

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1:9e63d5f02d62

<macros>

    <xml name="requirements">
        <requirements>
            <requirement type="package">pandas</requirement>
            <requirement type="package">scipy</requirement>
            <requirement type="package">cobrapy</requirement>
            <requirement type="package">python-libsbml</requirement>
        </requirements>
    </xml>

    <xml name="options">
        <param name="rules_selector" argument="--rules_selector" type="select" label="Gene-Protein-Reaction rules:">
            <option value="HMRcore" selected="true">HMRcore rules</option>
            <option value="Recon">Recon 2.2 rules</option>
            <option value="Custom">Custom rules</option>
        </param>
    </xml>

   <token name="@CUSTOM_RULES_EXEMPLE@">

+--------------------+-------------------------------+
|         id         |     rule (with entrez-id)     |
+====================+===============================+
|        SHMT1       |        155060 or 10357        |
+--------------------+-------------------------------+
|        NIT2        |      155060 or 100134869      |
+--------------------+-------------------------------+
| GOT1_GOT2_GOT1L1_2 | 155060 and 100134869 or 10357 |
+--------------------+-------------------------------+

|

    </token>

    <token name="@DATASET_EXEMPLE1@">

+------------+------------+------------+------------+   
|  Hugo_ID   | TCGAA62670 | TCGAA62671 | TCGAA62672 |   
+============+============+============+============+   
| HGNC:24086 |  0.523167  |  0.371355  |  0.925661  |   
+------------+------------+------------+------------+    
| HGNC:24086 |  0.568765  |  0.765567  |  0.456789  |    
+------------+------------+------------+------------+    
| HGNC:9876  |  0.876545  |  0.768933  |  0.987654  |   
+------------+------------+------------+------------+    
| HGNC:9     |  0.456788  |  0.876543  |  0.876542  |   
+------------+------------+------------+------------+    
| HGNC:23    |  0.876543  |  0.786543  |  0.897654  |   
+------------+------------+------------+------------+ 
   
|

    </token>

    <token name="@DATASET_EXEMPLE2@">

+-------------+------------+------------+------------+
| Hugo_Symbol | TCGAA62670 | TCGAA62671 | TCGAA62672 |
+=============+============+============+============+
|    A1BG     |  0.523167  |  0.371355  |  0.925661  |
+-------------+------------+------------+------------+
|    A1CF     |  0.568765  |  0.765567  |  0.456789  |
+-------------+------------+------------+------------+
|     A2M     |  0.876545  |  0.768933  |  0.987654  |
+-------------+------------+------------+------------+
|    A4GALT   |  0.456788  |  0.876543  |  0.876542  |
+-------------+------------+------------+------------+
|   M664Y65   |  0.876543  |  0.786543  |  0.897654  |
+-------------+------------+------------+------------+

|

    </token>

    <token name="@REFERENCE@">

This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_. Development team: Irene Sala, Luca Rosato, Davide Maspero, Chiara Damiani.

.. _BIMIB: http://sito di bio.org
.. _Department of Informatics, Systems and Communications: http://www.disco.unimib.it/go/Home/English
.. _University of Milan - Bicocca: https://www.unimib.it/

    </token>

    <xml name="citations">
        <citations> <!--esempio di citazione-->
            <citation type="bibtex">
@online{lh32017,
  author = {Alex Graudenzi, Davide Maspero, Cluadio Isella, Marzia Di Filippo, Giancarlo Mauri, Enzo Medico, Marco Antoniotti, Chiara Damiani},
  year = {2018},
  title = {MaREA: Metabolic feature extraction, enrichment and visualization of RNAseq},
  publisher = {bioRxiv},
  journal = {bioRxiv},
  url = {https://www.biorxiv.org/content/early/2018/01/16/248724},
}
            </citation>
        </citations>
    </xml>

</macros>