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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>