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comparison Desktop/Marea/marea_macros.xml @ 30:e88efefbd015 draft

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author bimib
date Tue, 15 Oct 2019 12:21:16 -0400
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29:9fcb0e8d6d47 30:e88efefbd015
1 <macros>
2
3 <xml name="options">
4 <param name="rules_selector" argument="--rules_selector" type="select" label="Gene-Protein-Reaction rules:">
5 <option value="HMRcore" selected="true">HMRcore rules</option>
6 <option value="Recon">Recon 2.2 rules</option>
7 <option value="Custom">Custom rules</option>
8 </param>
9 </xml>
10
11 <token name="@CUSTOM_RULES_EXEMPLE@">
12
13 +--------------------+-------------------------------+
14 | id | rule (with entrez-id) |
15 +====================+===============================+
16 | SHMT1 | 155060 or 10357 |
17 +--------------------+-------------------------------+
18 | NIT2 | 155060 or 100134869 |
19 +--------------------+-------------------------------+
20 | GOT1_GOT2_GOT1L1_2 | 155060 and 100134869 or 10357 |
21 +--------------------+-------------------------------+
22
23 |
24
25 </token>
26
27 <token name="@DATASET_EXEMPLE1@">
28
29 +------------+------------+------------+------------+
30 | Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 |
31 +============+============+============+============+
32 | HGNC:24086 | 0.523167 | 0.371355 | 0.925661 |
33 +------------+------------+------------+------------+
34 | HGNC:24086 | 0.568765 | 0.765567 | 0.456789 |
35 +------------+------------+------------+------------+
36 | HGNC:9876 | 0.876545 | 0.768933 | 0.987654 |
37 +------------+------------+------------+------------+
38 | HGNC:9 | 0.456788 | 0.876543 | 0.876542 |
39 +------------+------------+------------+------------+
40 | HGNC:23 | 0.876543 | 0.786543 | 0.897654 |
41 +------------+------------+------------+------------+
42
43 |
44
45 </token>
46
47 <token name="@DATASET_EXEMPLE2@">
48
49 +-------------+------------+------------+------------+
50 | Hugo_Symbol | TCGAA62670 | TCGAA62671 | TCGAA62672 |
51 +=============+============+============+============+
52 | A1BG | 0.523167 | 0.371355 | 0.925661 |
53 +-------------+------------+------------+------------+
54 | A1CF | 0.568765 | 0.765567 | 0.456789 |
55 +-------------+------------+------------+------------+
56 | A2M | 0.876545 | 0.768933 | 0.987654 |
57 +-------------+------------+------------+------------+
58 | A4GALT | 0.456788 | 0.876543 | 0.876542 |
59 +-------------+------------+------------+------------+
60 | M664Y65 | 0.876543 | 0.786543 | 0.897654 |
61 +-------------+------------+------------+------------+
62
63 |
64
65 </token>
66
67 <token name="@REFERENCE@">
68
69 This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_.
70
71 .. _BIMIB: http://sito di bio.org
72 .. _Department of Informatics, Systems and Communications: http://www.disco.unimib.it/go/Home/English
73 .. _University of Milan - Bicocca: https://www.unimib.it/
74
75 </token>
76
77 <xml name="citations">
78 <citations> <!--esempio di citazione-->
79 <citation type="bibtex">
80 @online{lh32017,
81 author = {Alex Graudenzi, Davide Maspero, Cluadio Isella, Marzia Di Filippo, Giancarlo Mauri, Enzo Medico, Marco Antoniotti, Chiara Damiani},
82 year = {2018},
83 title = {MaREA: Metabolic feature extraction, enrichment and visualization of RNAseq},
84 publisher = {bioRxiv},
85 journal = {bioRxiv},
86 url = {https://www.biorxiv.org/content/early/2018/01/16/248724},
87 }
88 </citation>
89 </citations>
90 </xml>
91
92 </macros>