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comparison COBRAxy/custom_data_generator.xml @ 6:deb6d3439342 draft

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author luca_milaz
date Wed, 18 Sep 2024 12:00:49 +0000
parents 41f35c2f0c7b
children c5dbdbb64cef
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5:aaad8c11b7d6 6:deb6d3439342
41 <help> 41 <help>
42 <![CDATA[ 42 <![CDATA[
43 What it does 43 What it does
44 ------------- 44 -------------
45 45
46 This tool generates two files containing reactions and rules respectively, starting from a custom model in JSON or XML format, that can be used as inputs for the RAS and RPS generator modules. 46 This tool generates four files containing reactions, rules, reaction bounds and medium composition respectively, starting from a custom model in JSON or XML format.
47 Reactions and rules can be used as inputs for the RAS and RPS generator tools.
47 48
48 Accepted files: 49 Accepted files:
49 - A model: JSON or XML file reporting reactions and rules contained in the model. 50 - A model: JSON or XML file reporting reactions and rules contained in the model.
50 51
51 52
53 ------------- 54 -------------
54 55
55 The tool generates: 56 The tool generates:
56 - rules: reporting the rules for each reaction in the custom model given. Format: csv or pickle. 57 - rules: reporting the rules for each reaction in the custom model given. Format: csv or pickle.
57 - reactions: reporting the reactions in the custom model given. Format: csv or pickle. 58 - reactions: reporting the reactions in the custom model given. Format: csv or pickle.
59 - reaction bounds: reporting the lower and upper bounds of each model reaction. Format: csv or pickle.
60 - medium composition: reporting the list of exchange/transport reactions. Format: csv or pickle.
58 - a log file (.txt). 61 - a log file (.txt).
59 ]]> 62 ]]>
60 </help> 63 </help>
61 <expand macro="citations" /> 64 <expand macro="citations" />
62 </tool> 65 </tool>