<macros>

    <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="ENGRO2">ENGRO 2 rules</option>
            <option value="Custom">Custom rules</option>
        </param>
    </xml>

    <xml name="options_ras_to_bounds_model">
        <param name="model_selector" argument="--model_selector" type="select" label="Model:">
            <option value="ENGRO2">ENGRO 2</option>
            <option value="Custom">Custom model</option>
        </param>
    </xml>

    <xml name="options_ras_to_bounds_medium">
        <param name="medium_selector" argument="--medium_selector" type="select" label="Medium:">
            <option value="allOpen">Open</option>
            <option value="Custom">Custom medium</option>
            <option value="RPMI_1640">RPMI 1640</option>
            <option value="DMEM">DMEM</option>
            <option value="EMEM">EMEM</option>
            <option value="DMEM:F12_=_1:1">DMEM:F12 = 1:1</option>
            <option value="McCoy's_5A">McCoy's 5A</option>
            <option value="IMDM">IMDM</option>
            <option value="MEM">MEM</option>
            <option value="GMEM">GMEM</option>
            <option value="Leibovitz's_L-15">Leibovitz's L-15</option>
            <option value="F12">F12</option>
            <option value="F10">F10</option>
            <option value="AMEM">AMEM</option>
            <option value="Waymouth_MB_7521_medium">Waymouth MB 7521 medium</option>
            <option value="F12K">F12K</option>
            <option value="William's_E_Medium">William's E Medium</option>
            <option value="Medium_199">Medium 199</option>
            <option value="MCDB_105">MCDB 105</option>
            <option value="NEAA">NEAA</option>
            <option value="RPMI:F12_=_1:1">RPMI:F12 = 1:1</option>
            <option value="RPMI:MEM_=_1:1">RPMI:MEM = 1:1</option>
            <option value="RPMI:EMEM_=_1:1">RPMI:EMEM = 1:1</option>
            <option value="EMEM:F12_=_1:1">EMEM:F12 = 1:1</option>
            <option value="DMEM:RPMI_=_2:1">DMEM:RPMI = 2:1</option>
            <option value="DMEM:IMDM_=_1:1">DMEM:IMDM = 1:1</option>
            <option value="MCDB_105:Medium_199_=_1:1">MCDB 105:Medium 199 = 1:1</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`_.

.. _BIMIB: https://bimib.disco.unimib.it/index.php/Home
.. _Department of Informatics, Systems and Communications: https://www.disco.unimib.it/en
.. _University of Milan - Bicocca: https://en.unimib.it/

    </token>

    <xml name="citations">
        <citations> <!--esempio di citazione-->
            <citation type="bibtex">
              @article{graudenzi2018integration,
              title={Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power},
              author={Graudenzi, Alex and Maspero, Davide and Di Filippo, Marzia and Gnugnoli, Marco and Isella, Claudio and Mauri, Giancarlo and Medico, Enzo and Antoniotti, Marco and Damiani, Chiara},
              journal={Journal of biomedical informatics},
              volume={87},
              pages={37--49},
              year={2018},
              publisher={Elsevier},
              url = {https://doi.org/10.1016/j.jbi.2018.09.010},
              }
            </citation>
            <citation type="bibtex">
              @article{damiani2020marea4galaxy,
              title={MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy},
              author={Damiani, Chiara and Rovida, Lorenzo and Maspero, Davide and Sala, Irene and Rosato, Luca and Di Filippo, Marzia and Pescini, Dario and Graudenzi, Alex and Antoniotti, Marco and Mauri, Giancarlo},
              journal={Computational and Structural Biotechnology Journal},
              volume={18},
              pages={993},
              year={2020},
              publisher={Research Network of Computational and Structural Biotechnology},
              url = {https://doi.org/10.1016/j.csbj.2020.04.008},
              }
            </citation>
            <citation type="bibtex">
              @article{ebrahim2013cobrapy,
                title={COBRApy: constraints-based reconstruction and analysis for python},
                author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
                journal={BMC systems biology},
                volume={7},
                pages={1--6},
                year={2013},
                publisher={Springer}
                }
            </citation>
        </citations>
    </xml>

    <xml name="citations_fluxes">
        <citations>
        <citation type="bibtex">
                @article{galuzzi2024adjusting,
                title={Adjusting for false discoveries in constraint-based differential metabolic flux analysis},
                author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara},
                journal={Journal of Biomedical Informatics},
                volume={150},
                pages={104597},
                year={2024},
                publisher={Elsevier}
                }
            </citation>
            <citation type="bibtex">
                @inproceedings{galuzzi2022best,
                title={Best practices in flux sampling of constrained-based models},
                author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara},
                booktitle={International Conference on Machine Learning, Optimization, and Data Science},
                pages={234--248},
                year={2022},
                organization={Springer}
                }
            </citation>
            <citation type="bibtex">
                @article{ebrahim2013cobrapy,
                    title={COBRApy: constraints-based reconstruction and analysis for python},
                    author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
                    journal={BMC systems biology},
                    volume={7},
                    pages={1--6},
                    year={2013},
                    publisher={Springer}
                    }
            </citation>
        </citations>
    </xml>


</macros>