Mercurial > repos > bimib > marea
view Marea/marea_macros.xml @ 88:66432fdf1768 draft
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author | bimib |
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date | Mon, 07 Jun 2021 14:15:08 +0000 |
parents | 500c9e788a05 |
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<macros> <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`_. .. _BIMIB: https://bimib.disco.unimib.it/index.php/Home .. _Department of Informatics, Systems and Communications: https://www.disco.unimib.it/en .. _University of Milan - Bicocca: https://en.unimib.it/ </token> <xml name="citations"> <citations> <!--esempio di citazione--> <citation type="bibtex"> @article{graudenzi2018integration, title={Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power}, 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}, journal={Journal of biomedical informatics}, volume={87}, pages={37--49}, year={2018}, publisher={Elsevier}, url = {https://doi.org/10.1016/j.jbi.2018.09.010}, } </citation> <citation type="bibtex"> @article{damiani2020marea4galaxy, title={MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy}, 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}, journal={Computational and Structural Biotechnology Journal}, volume={18}, pages={993}, year={2020}, publisher={Research Network of Computational and Structural Biotechnology}, url = {https://doi.org/10.1016/j.csbj.2020.04.008}, } </citation> </citations> </xml> </macros>