Mercurial > repos > bimib > marea_2
view marea_2/custom_data_generator.xml @ 328:b182c46206e2 draft
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author | luca_milaz |
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date | Mon, 05 Aug 2024 19:32:16 +0000 |
parents | 77fa38217b6f |
children | 0312366eabfd |
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<tool id="MaREA Custom Data Generator" name="CustomDataGenerator" version="2.0.0"> <macros> <import>marea_macros.xml</import> </macros> <requirements> <requirement type="package" version="1.24.4">numpy</requirement> <requirement type="package" version="2.0.3">pandas</requirement> <requirement type="package" version="0.29.0">cobra</requirement> <requirement type="package" version="5.2.2">lxml</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ python $__tool_directory__/custom_data_generator.py --input $input --name $input.element_identifier --out_log $log --bounds $bounds --reactions $reactions --medium $medium --rules $rules ]]> </command> <inputs> <param name="input" argument="--input" type="data" format="xml, json" label="Custom model:" /> <param name="name" argument="--name" type="text" label="Model's name:" value="Model" help="Default: Model" /> </inputs> <outputs> <data format="txt" name="log" label="CustomDataGenerator - $name - Log" /> <data format="tabular" name="bounds" label="${tool.name} Bounds" /> <data format="tabular" name="reactions" label="${tool.name} Reactions" /> <data format="tabular" name="medium" label="${tool.name} Medium" /> <data format="tabular" name="rules" label="${tool.name} Rules" /> </outputs> <help> <![CDATA[ What it does ------------- 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. Accepted files: - A model: JSON or XML file reporting reactions and rules contained in the model. Output: ------------- The tool generates: - rules: reporting the rules for each reaction in the custom model given. Format: csv or pickle. - reactions: reporting the reactions in the custom model given. Format: csv or pickle. - a log file (.txt). ]]> </help> <expand macro="citations" /> </tool>