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changeset 488:e0bcc61b2feb draft default tip

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Uploaded
author luca_milaz
date Tue, 23 Sep 2025 13:48:24 +0000
parents 6b8a7e1e8efa
children
files COBRAxy/marea_macros.xml
diffstat 1 files changed, 210 insertions(+), 203 deletions(-) [+]
line wrap: on
line diff
--- a/COBRAxy/marea_macros.xml	Tue Sep 23 13:48:06 2025 +0000
+++ b/COBRAxy/marea_macros.xml	Tue Sep 23 13:48:24 2025 +0000
@@ -1,203 +1,210 @@
-<macros>
-
-    <xml name="options">
-        <param name="rules_selector" argument="--rules_selector" type="select" label="Gene-Protein-Reaction rules:">
-            <option value="HMRcore">HMRcore tabular</option>
-            <option value="Recon">Recon3D tabular</option>
-            <option value="ENGRO2"  selected="true">ENGRO 2 tabular</option>
-            <option value="Custom">Custom rules</option>
-        </param>
-    </xml>
-
-    <xml name="options_model">
-        <param name="model_selector" argument="--model_selector" type="select" label="Model:">
-            <option value="ENGRO2"  selected="true">ENGRO 2 tabular</option>
-            <option value="Recon">Recon3D tabular</option>
-            <option value="Custom_model">Custom tabular</option>
-        </param>
-    </xml>
-
-    <xml name="options_ras_to_bounds_model">
-        <param name="model_selector" argument="--model_selector" type="select" label="Model:">
-            <option value="ENGRO2"  selected="true">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="Default" selected="true">Default (ENGRO2 built-in medium)</option>
-            <option value="allOpen">Open</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>
+<macros>
+
+    <xml name="options">
+        <param name="rules_selector" argument="--rules_selector" type="select" label="Gene-Protein-Reaction rules:">
+            <option value="HMRcore">HMRcore tabular</option>
+            <option value="Recon">Recon3D tabular</option>
+            <option value="ENGRO2"  selected="true">ENGRO 2 tabular</option>
+            <option value="Custom">Custom rules</option>
+        </param>
+    </xml>
+
+    <xml name="options_model">
+        <param name="model_selector" argument="--model_selector" type="select" label="Model:">
+            <option value="ENGRO2"  selected="true">ENGRO 2 tabular</option>
+            <option value="Recon">Recon3D tabular</option>
+            <option value="Custom_model">Custom tabular</option>
+        </param>
+    </xml>
+
+    <xml name="options_ras_to_bounds_model">
+        <param name="model_selector" argument="--model_selector" type="select" label="Model:">
+            <option value="ENGRO2"  selected="true">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="Default" selected="true">Default (ENGRO2 built-in medium)</option>
+            <option value="allOpen">Open</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="adv_DMEM:F12_=_1:1">adv 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="mIVC1:adv_DMEM:F12_=_1:1">mIVC1:adv DMEM:F12 = 1:1</option>
+            <option value="E8_ess">E8 ess</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>
+            <option value="mIVC1:adv_DMEM:F12_=_1:1_open">mIVC1:adv DMEM:F12 = 1:1 open</option>
+            <option value="E8_ess_open">E8 ess open</option>
+            <option value="open_10">Open 10</option>
+            <option value="E8_open_10">E8 open 10</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>