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comparison COBRAxy/ras_to_bounds.xml @ 82:226bee471503 draft

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Uploaded
author luca_milaz
date Sun, 13 Oct 2024 11:03:02 +0000
parents a30013ece710
children bfb17674d13b
comparison
equal deleted inserted replaced
81:a30013ece710 82:226bee471503
27 --medium $medium 27 --medium $medium
28 #end if 28 #end if
29 --ras_selector $cond_ras.ras_choice 29 --ras_selector $cond_ras.ras_choice
30 #if $cond_ras.ras_choice == "True" 30 #if $cond_ras.ras_choice == "True"
31 --input_ras $cond_ras.input_ras 31 --input_ras $cond_ras.input_ras
32 #set $names = ""
33 #for $input_temp in $cond_ras.input_ras:
34 #set $names = $names + $input_temp.element_identifier + ","
35 #end for
36 --names $names
32 #end if 37 #end if
33 --out_log $log 38 --out_log $log
34 ]]> 39 ]]>
35 </command> 40 </command>
36 <inputs> 41 <inputs>
83 Accepted files: 88 Accepted files:
84 - A model: JSON or XML file reporting reactions and rules contained in the model. 89 - A model: JSON or XML file reporting reactions and rules contained in the model.
85 - RAS matrix: tab-separated RAS file as returned by RAS generator. Multiple RAS files can be uploaded too (e.g. one RAS matrix for normal cells and one for cancer cells). Note that if multiple RAs matrices are uploaded, the bounds are normalzed across all cells. 90 - RAS matrix: tab-separated RAS file as returned by RAS generator. Multiple RAS files can be uploaded too (e.g. one RAS matrix for normal cells and one for cancer cells). Note that if multiple RAs matrices are uploaded, the bounds are normalzed across all cells.
86 - Medium: tab-separated file containing lower and upper-bounds of medium reactions. 91 - Medium: tab-separated file containing lower and upper-bounds of medium reactions.
87 92
88 Example of custum growth medium fileeeee: 93 Example of custum growth medium file:
89 94
90 95
91 +------------+----------------+----------------+ 96 +------------+----------------+----------------+
92 | Reaction ID| lower_bound | upper_bound | 97 | Reaction ID| lower_bound | upper_bound |
93 +============+================+================+ 98 +============+================+================+
96 | r2 | 0.268765 | 0.765567 | 101 | r2 | 0.268765 | 0.765567 |
97 +------------+----------------+----------------+ 102 +------------+----------------+----------------+
98 103
99 Example for multiple RAS matrices: 104 Example for multiple RAS matrices:
100 - cancer.csv and normal.csv generated by RAS generator tool (the two class names are 'cancer' and 'normal'). 105 - cancer.csv and normal.csv generated by RAS generator tool (the two class names are 'cancer' and 'normal').
101 - This tool returns one unique collection of bounds files for both cancer and normal cells (normalization is performed across all cells). 106 +
107 − - This tool returns one unique collection of bounds files for both cancer and normal cells (normalization is performed across all cells).
102 - The association cell-class is reported in the 'cell_class' file that is useful to perform flux enrichment analysis based on class partenrship. 108 - The association cell-class is reported in the 'cell_class' file that is useful to perform flux enrichment analysis based on class partenrship.
103 109
104 Output: 110 Output:
105 ------------- 111 -------------
106 112