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