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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Marea/marea_macros.xml	Wed Nov 07 07:07:46 2018 -0500
@@ -0,0 +1,101 @@
+<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>