Mercurial > repos > bimib > cobraxy

comparison COBRAxy/ras_to_bounds.xml @ 99:9f1a751652fc draft

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Uploaded
author luca_milaz
date Sun, 13 Oct 2024 11:54:36 +0000
parents a695435aa879
children c7bdcfbb575c
comparison
equal deleted inserted replaced
98:54ded7f28a60 99:9f1a751652fc
29 --ras_selector $cond_ras.ras_choice 29 --ras_selector $cond_ras.ras_choice
30 #set $names = "" 30 #set $names = ""
31 #if $cond_ras.ras_choice == "True" 31 #if $cond_ras.ras_choice == "True"
32 --input_ras $cond_ras.input_ras 32 --input_ras $cond_ras.input_ras
33 #for $input_temp in $cond_ras.input_ras: 33 #for $input_temp in $cond_ras.input_ras:
34 #set $names = $names + $input_temp.element_identifier + "," 34 #set $names = $names + $input_temp.element_identifier
35 #end for 35 #end for
36 #end if 36 #end if
37 --name $names 37 --name $names
38 --out_log $log 38 --out_log $log
39 ]]> 39 ]]>
88 Accepted files: 88 Accepted files:
89 - 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.
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. 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.
91 - 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.
92 92
93 Example of custum growth medium fileeeee: 93 Example of custum growth medium file:
94 94
95 95
96 +------------+----------------+----------------+ 96 +------------+----------------+----------------+
97 | Reaction ID| lower_bound | upper_bound | 97 | Reaction ID| lower_bound | upper_bound |
98 +============+================+================+ 98 +============+================+================+