Mercurial > repos > bimib > cobraxy
changeset 346:0ac89744208f draft
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--- a/custom_data_generator.xml Thu Sep 04 22:10:56 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -<tool id="CustomDataGenerator" name="Custom Data Generator" 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 - --medium_selector $cond_medium.medium_selector - --output_format $output_format - #if $cond_model.model_selector == 'Custom_model' - --input $cond_model.input - --name $cond_model.name - #else - --model $cond_model.model_selector - --name $cond_model.model_selector - #end if - #if $cond_medium.medium_selector == 'Custom' - --medium $cond_medium.medium - #end if - --out_log $log - --out_data $out_data - ]]> - </command> - <inputs> - <!-- modello --> - <conditional name="cond_model"> - <expand macro="options_model"/> - <when value="Custom_model"> - <param name="input" argument="--input" type="data" format="json,xml" label="Custom model file:" /> - <param name="name" argument="--name" type="text" label="Model's name:" value="CustomModel" help="Default: CustomModel. Do not use spaces or special symbols." /> - </when> - </conditional> - - <!-- formato output --> - <param name="output_format" argument="--output_format" type="select" label="Output format:"> - <option value="tabular" selected="true">CSV (tabular)</option> - <option value="xlsx">Excel (.xlsx)</option> - </param> - - <!-- medium --> - <conditional name="cond_medium"> - <expand macro="options_ras_to_bounds_medium"/> - <when value="Custom"> - <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" /> - </when> - </conditional> - </inputs> - - <outputs> - <data name="log" format="txt" label="CustomDataGenerator - Log" /> - <data name="out_data" format="$output_format" label="${cond_model.model_selector}_data" /> - </outputs> - - <help> - <![CDATA[ -What it does -------------- - -This tool generates four files containing reactions, rules, reaction bounds and medium composition respectively, starting from a custom model in JSON or XML format. -Reactions and rules can be used as inputs for the RAS and RPS generator tools. - -Accepted files: - - A model: JSON or XML file reporting reactions and rules contained in the model. Supported compressed formats: .zip, .gz and .bz2 - Filename must end with .json.zip (.xml.zip), .json.gz (.xml.gz) or .json.bz2 (.xml.bz2) for JSON (XML) files. - - -Output: -------------- - -The tool generates: - - rules: reporting the rules for each reaction in the custom model given. Format: csv (tab separated). - - reactions: reporting the reactions in the custom model given. Format: csv (tab separated). - - reaction bounds: reporting the lower and upper bounds of each model reaction. Format: csv (tab separated). - - medium composition: reporting the list of exchange/transport reactions. Format: csv (tab separated). - - a log file (.txt). - ]]> - </help> - <expand macro="citations" /> -</tool> \ No newline at end of file