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93
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1 <macros>
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2
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3 <xml name="options">
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4 <param name="rules_selector" argument="--rules_selector" type="select" label="Gene-Protein-Reaction rules:">
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5 <option value="HMRcore" selected="true">HMRcore rules</option>
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6 <option value="Recon">Recon 2.2 rules</option>
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7 <option value="ENGRO2">ENGRO 2 rules</option>
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8 <option value="Custom">Custom rules</option>
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9 </param>
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10 </xml>
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11
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12 <xml name="options_ras_to_bounds_model">
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13 <param name="model_selector" argument="--model_selector" type="select" label="Model:">
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14 <option value="ENGRO2">ENGRO 2</option>
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15 <option value="Custom">Custom model</option>
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16 </param>
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17 </xml>
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18
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19 <xml name="options_ras_to_bounds_medium">
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20 <param name="medium_selector" argument="--medium_selector" type="select" label="Medium:">
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21 <option value="allOpen">Open</option>
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22 <option value="Custom">Custom medium</option>
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23 <option value="RPMI_1640">RPMI 1640</option>
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24 <option value="DMEM">DMEM</option>
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25 <option value="EMEM">EMEM</option>
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26 <option value="DMEM:F12_=_1:1">DMEM:F12 = 1:1</option>
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27 <option value="McCoy's_5A">McCoy's 5A</option>
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28 <option value="IMDM">IMDM</option>
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29 <option value="MEM">MEM</option>
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30 <option value="GMEM">GMEM</option>
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31 <option value="Leibovitz's_L-15">Leibovitz's L-15</option>
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32 <option value="F12">F12</option>
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33 <option value="F10">F10</option>
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34 <option value="AMEM">AMEM</option>
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35 <option value="Waymouth_MB_7521_medium">Waymouth MB 7521 medium</option>
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36 <option value="F12K">F12K</option>
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37 <option value="William's_E_Medium">William's E Medium</option>
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38 <option value="Medium_199">Medium 199</option>
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39 <option value="MCDB_105">MCDB 105</option>
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40 <option value="NEAA">NEAA</option>
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41 <option value="RPMI:F12_=_1:1">RPMI:F12 = 1:1</option>
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42 <option value="RPMI:MEM_=_1:1">RPMI:MEM = 1:1</option>
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43 <option value="RPMI:EMEM_=_1:1">RPMI:EMEM = 1:1</option>
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44 <option value="EMEM:F12_=_1:1">EMEM:F12 = 1:1</option>
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45 <option value="DMEM:RPMI_=_2:1">DMEM:RPMI = 2:1</option>
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46 <option value="DMEM:IMDM_=_1:1">DMEM:IMDM = 1:1</option>
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47 <option value="MCDB_105:Medium_199_=_1:1">MCDB 105:Medium 199 = 1:1</option>
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48 </param>
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49 </xml>
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50
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51 <token name="@CUSTOM_RULES_EXEMPLE@">
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52
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53 +--------------------+-------------------------------+
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54 | id | rule (with entrez-id) |
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55 +====================+===============================+
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56 | SHMT1 | 155060 or 10357 |
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57 +--------------------+-------------------------------+
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58 | NIT2 | 155060 or 100134869 |
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59 +--------------------+-------------------------------+
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60 | GOT1_GOT2_GOT1L1_2 | 155060 and 100134869 or 10357 |
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61 +--------------------+-------------------------------+
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62
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63 |
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64
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65 </token>
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66
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67 <token name="@DATASET_EXEMPLE1@">
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68
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69 +------------+------------+------------+------------+
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70 | Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 |
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71 +============+============+============+============+
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72 | HGNC:24086 | 0.523167 | 0.371355 | 0.925661 |
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73 +------------+------------+------------+------------+
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74 | HGNC:24086 | 0.568765 | 0.765567 | 0.456789 |
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75 +------------+------------+------------+------------+
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76 | HGNC:9876 | 0.876545 | 0.768933 | 0.987654 |
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77 +------------+------------+------------+------------+
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78 | HGNC:9 | 0.456788 | 0.876543 | 0.876542 |
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79 +------------+------------+------------+------------+
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80 | HGNC:23 | 0.876543 | 0.786543 | 0.897654 |
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81 +------------+------------+------------+------------+
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82
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83 |
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84
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85 </token>
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86
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87 <token name="@DATASET_EXEMPLE2@">
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88
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89 +-------------+------------+------------+------------+
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90 | Hugo_Symbol | TCGAA62670 | TCGAA62671 | TCGAA62672 |
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91 +=============+============+============+============+
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92 | A1BG | 0.523167 | 0.371355 | 0.925661 |
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93 +-------------+------------+------------+------------+
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94 | A1CF | 0.568765 | 0.765567 | 0.456789 |
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95 +-------------+------------+------------+------------+
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96 | A2M | 0.876545 | 0.768933 | 0.987654 |
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97 +-------------+------------+------------+------------+
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98 | A4GALT | 0.456788 | 0.876543 | 0.876542 |
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99 +-------------+------------+------------+------------+
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100 | M664Y65 | 0.876543 | 0.786543 | 0.897654 |
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101 +-------------+------------+------------+------------+
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102
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103 |
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104
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105 </token>
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106
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107 <token name="@REFERENCE@">
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108
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109 This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_.
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110
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111 .. _BIMIB: https://bimib.disco.unimib.it/index.php/Home
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112 .. _Department of Informatics, Systems and Communications: https://www.disco.unimib.it/en
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113 .. _University of Milan - Bicocca: https://en.unimib.it/
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114
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115 </token>
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116
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117 <xml name="citations">
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118 <citations> <!--esempio di citazione-->
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119 <citation type="bibtex">
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120 @article{graudenzi2018integration,
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121 title={Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power},
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122 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},
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123 journal={Journal of biomedical informatics},
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124 volume={87},
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125 pages={37--49},
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126 year={2018},
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127 publisher={Elsevier},
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128 url = {https://doi.org/10.1016/j.jbi.2018.09.010},
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129 }
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130 </citation>
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131 <citation type="bibtex">
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132 @article{damiani2020marea4galaxy,
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133 title={MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy},
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134 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},
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135 journal={Computational and Structural Biotechnology Journal},
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136 volume={18},
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137 pages={993},
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138 year={2020},
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139 publisher={Research Network of Computational and Structural Biotechnology},
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140 url = {https://doi.org/10.1016/j.csbj.2020.04.008},
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141 }
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142 </citation>
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143 <citation type="bibtex">
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144 @article{ebrahim2013cobrapy,
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145 title={COBRApy: constraints-based reconstruction and analysis for python},
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146 author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
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147 journal={BMC systems biology},
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148 volume={7},
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149 pages={1--6},
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150 year={2013},
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151 publisher={Springer}
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152 }
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153 </citation>
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154 </citations>
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155 </xml>
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156
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157 <xml name="citations_fluxes">
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158 <citations>
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159 <citation type="bibtex">
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160 @article{galuzzi2024adjusting,
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161 title={Adjusting for false discoveries in constraint-based differential metabolic flux analysis},
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162 author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara},
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163 journal={Journal of Biomedical Informatics},
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164 volume={150},
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165 pages={104597},
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166 year={2024},
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167 publisher={Elsevier}
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168 }
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169 </citation>
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170 <citation type="bibtex">
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171 @inproceedings{galuzzi2022best,
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172 title={Best practices in flux sampling of constrained-based models},
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173 author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara},
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174 booktitle={International Conference on Machine Learning, Optimization, and Data Science},
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175 pages={234--248},
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176 year={2022},
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177 organization={Springer}
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178 }
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179 </citation>
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180 <citation type="bibtex">
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181 @article{ebrahim2013cobrapy,
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182 title={COBRApy: constraints-based reconstruction and analysis for python},
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183 author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
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184 journal={BMC systems biology},
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185 volume={7},
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186 pages={1--6},
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187 year={2013},
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188 publisher={Springer}
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189 }
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190 </citation>
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191 </citations>
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192 </xml>
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193
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194
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195 </macros>
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