Mercurial > repos > bimib > marea

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bimib
date Wed, 07 Nov 2018 07:07:46 -0500
parents
children 3b3d0e5d0802
comparison
equal deleted inserted replaced
0:23ac9cf12788 1:9e63d5f02d62
1 <macros>
2
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package">pandas</requirement>
6 <requirement type="package">scipy</requirement>
7 <requirement type="package">cobrapy</requirement>
8 <requirement type="package">python-libsbml</requirement>
9 </requirements>
10 </xml>
11
12 <xml name="options">
13 <param name="rules_selector" argument="--rules_selector" type="select" label="Gene-Protein-Reaction rules:">
14 <option value="HMRcore" selected="true">HMRcore rules</option>
15 <option value="Recon">Recon 2.2 rules</option>
16 <option value="Custom">Custom rules</option>
17 </param>
18 </xml>
19
20 <token name="@CUSTOM_RULES_EXEMPLE@">
21
22 +--------------------+-------------------------------+
23 | id | rule (with entrez-id) |
24 +====================+===============================+
25 | SHMT1 | 155060 or 10357 |
26 +--------------------+-------------------------------+
27 | NIT2 | 155060 or 100134869 |
28 +--------------------+-------------------------------+
29 | GOT1_GOT2_GOT1L1_2 | 155060 and 100134869 or 10357 |
30 +--------------------+-------------------------------+
31
32 |
33
34 </token>
35
36 <token name="@DATASET_EXEMPLE1@">
37
38 +------------+------------+------------+------------+
39 | Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 |
40 +============+============+============+============+
41 | HGNC:24086 | 0.523167 | 0.371355 | 0.925661 |
42 +------------+------------+------------+------------+
43 | HGNC:24086 | 0.568765 | 0.765567 | 0.456789 |
44 +------------+------------+------------+------------+
45 | HGNC:9876 | 0.876545 | 0.768933 | 0.987654 |
46 +------------+------------+------------+------------+
47 | HGNC:9 | 0.456788 | 0.876543 | 0.876542 |
48 +------------+------------+------------+------------+
49 | HGNC:23 | 0.876543 | 0.786543 | 0.897654 |
50 +------------+------------+------------+------------+
51
52 |
53
54 </token>
55
56 <token name="@DATASET_EXEMPLE2@">
57
58 +-------------+------------+------------+------------+
59 | Hugo_Symbol | TCGAA62670 | TCGAA62671 | TCGAA62672 |
60 +=============+============+============+============+
61 | A1BG | 0.523167 | 0.371355 | 0.925661 |
62 +-------------+------------+------------+------------+
63 | A1CF | 0.568765 | 0.765567 | 0.456789 |
64 +-------------+------------+------------+------------+
65 | A2M | 0.876545 | 0.768933 | 0.987654 |
66 +-------------+------------+------------+------------+
67 | A4GALT | 0.456788 | 0.876543 | 0.876542 |
68 +-------------+------------+------------+------------+
69 | M664Y65 | 0.876543 | 0.786543 | 0.897654 |
70 +-------------+------------+------------+------------+
71
72 |
73
74 </token>
75
76 <token name="@REFERENCE@">
77
78 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.
79
80 .. _BIMIB: http://sito di bio.org
81 .. _Department of Informatics, Systems and Communications: http://www.disco.unimib.it/go/Home/English
82 .. _University of Milan - Bicocca: https://www.unimib.it/
83
84 </token>
85
86 <xml name="citations">
87 <citations> <!--esempio di citazione-->
88 <citation type="bibtex">
89 @online{lh32017,
90 author = {Alex Graudenzi, Davide Maspero, Cluadio Isella, Marzia Di Filippo, Giancarlo Mauri, Enzo Medico, Marco Antoniotti, Chiara Damiani},
91 year = {2018},
92 title = {MaREA: Metabolic feature extraction, enrichment and visualization of RNAseq},
93 publisher = {bioRxiv},
94 journal = {bioRxiv},
95 url = {https://www.biorxiv.org/content/early/2018/01/16/248724},
96 }
97 </citation>
98 </citations>
99 </xml>
100
101 </macros>