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comparison COBRAxy/custom_data_generator.xml @ 93:7e703e546998 draft

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author luca_milaz
date Sun, 13 Oct 2024 11:41:34 +0000
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1 <tool id="CustomDataGenerator" name="Custom Data Generator" version="2.0.0">
2
3 <macros>
4 <import>marea_macros.xml</import>
5 </macros>
6
7 <requirements>
8 <requirement type="package" version="1.24.4">numpy</requirement>
9 <requirement type="package" version="2.0.3">pandas</requirement>
10 <requirement type="package" version="0.29.0">cobra</requirement>
11 <requirement type="package" version="5.2.2">lxml</requirement>
12 </requirements>
13
14 <command detect_errors="exit_code">
15 <![CDATA[
16 python $__tool_directory__/custom_data_generator.py
17 --input $input
18 --name $input.element_identifier
19 --out_log $log
20 --out_rules $rules
21 --out_reactions $reactions
22 --out_bounds $bounds
23 --out_medium $medium
24 ]]>
25 </command>
26 <inputs>
27 <param name="input" argument="--input" type="data" format="xml, json" label="Custom model:" />
28 <param name="name" argument="--name" type="text" label="Model's name:" value="Model" help="Default: Model" />
29 </inputs>
30
31 <outputs>
32 <data format="txt" name="log" label="${tool.name} - Log" />
33 <data format="tabular" name="rules" label="${name}_Rules" />
34 <data format="tabular" name="reactions" label="${name}_Reactions" />
35 <data format="tabular" name="bounds" label="${name}_Bounds" />
36 <data format="tabular" name="medium" label="${name}_Medium" />
37 </outputs>
38
39 <help>
40 <![CDATA[
41 What it does
42 -------------
43
44 This tool generates four files containing reactions, rules, reaction bounds and medium composition respectively, starting from a custom model in JSON or XML format.
45 Reactions and rules can be used as inputs for the RAS and RPS generator tools.
46
47 Accepted files:
48 - A model: JSON or XML file reporting reactions and rules contained in the model.
49
50
51 Output:
52 -------------
53
54 The tool generates:
55 - rules: reporting the rules for each reaction in the custom model given. Format: csv (tab separated).
56 - reactions: reporting the reactions in the custom model given. Format: csv (tab separated).
57 - reaction bounds: reporting the lower and upper bounds of each model reaction. Format: csv (tab separated).
58 - medium composition: reporting the list of exchange/transport reactions. Format: csv (tab separated).
59 - a log file (.txt).
60 ]]>
61 </help>
62 <expand macro="citations" />
63 </tool>