Mercurial > repos > bimib > cobraxy
changeset 385:cbb2dcbe768c draft
Uploaded
author | francesco_lapi |
---|---|
date | Fri, 05 Sep 2025 10:08:39 +0000 |
parents | 8a1213d1393d |
children | cccbf259459e |
files | COBRAxy/custom_data_generator.xml |
diffstat | 1 files changed, 137 insertions(+), 8 deletions(-) [+] |
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--- a/COBRAxy/custom_data_generator.xml Fri Sep 05 09:53:40 2025 +0000 +++ b/COBRAxy/custom_data_generator.xml Fri Sep 05 10:08:39 2025 +0000 @@ -4,18 +4,18 @@ <import>marea_macros.xml</import> </macros> - <requirements> + <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="0.29.0">cobra</requirement> <requirement type="package" version="5.2.2">lxml</requirement> - </requirements> + </requirements> <command detect_errors="exit_code"> <![CDATA[ - python $__tool_directory__/custom_data_generator.py + python $__tool_directory__/custom_data_generator.py --tool_dir $__tool_directory__ - --medium_selector $cond_medium.medium_selector + --medium_selector $cond_model.medium_selector #if $cond_model.model_selector == 'Custom_model' --input $cond_model.input --name $cond_model.name @@ -23,8 +23,8 @@ --model $cond_model.model_selector --name $cond_model.model_selector #end if - #if $cond_medium.medium_selector == 'Custom' - --medium $cond_medium.medium + #if $cond_model.medium_selector == 'Custom' + --medium $cond_model.medium #end if --out_log $log --out_tabular $out_tabular @@ -100,7 +100,136 @@ <data name="out_tabular" format="tabular" label="${cond_model.model_selector}_data_tabular" - optional="true"/> + optional="true"/> + </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, XML, MAT or YAML (.yml) file reporting reactions and rules contained in the model. Supported compressed formats: .zip, .gz and .bz2. Filename must follow the pattern: {model_name}.{extension}.[zip|gz|bz2] + +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><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 + --tool_dir $__tool_directory__ + --medium_selector $cond_model.medium_selector + #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_model.medium_selector == 'Custom' + --medium $cond_model.medium + #end if + --out_log $log + --out_tabular $out_tabular + ]]> + </command> + <inputs> + <conditional name="cond_model"> + <param name="model_selector" argument="--model_selector" type="select" label="Model:"> + <option value="HMRcore">HMRcore</option> + <option value="Recon">Recon 2.2</option> + <option value="ENGRO2" selected="true">ENGRO 2</option> + <option value="Custom_model">Custom</option> + </param> + <!-- ENGRO2 --> + <when value="ENGRO2"> + <param name="name" argument="--name" type="text" value="ENGRO2" hidden="true" /> + <conditional name="medium_selector"> + <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> + </when> + + <!-- Recon --> + <when value="Recon"> + <param name="name" argument="--name" type="text" value="Recon" hidden="true" /> + <param name="medium_selector" argument="--medium_selector" type="select" label="Medium"> + <option value="Default" selected="true">Default (Recon built-in medium)</option> + <option value="Custom">Custom medium file</option> + </param> + <conditional name="medium_selector"> + <when value="Custom"> + <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" /> + </when> + </conditional> + </when> + + <!-- HMRcore --> + <when value="HMRcore"> + <param name="name" argument="--name" type="text" value="HMRcore" hidden="true" /> + <param name="medium_selector" argument="--medium_selector" type="select" label="Medium"> + <option value="Default" selected="true">Default (HMRcore built-in medium)</option> + <option value="Custom">Custom medium file</option> + </param> + <conditional name="medium_selector"> + <when value="Custom"> + <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" /> + </when> + </conditional> + </when> + + <!-- Custom 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" /> + <param name="medium_selector" argument="--medium_selector" type="select" label="Medium"> + <option value="Default" selected="true">Don't use a separate medium file (use model defaults)</option> + <option value="Custom">Custom medium file (required)</option> + </param> + <conditional name="medium_selector"> + <when value="Custom"> + <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" /> + </when> + </conditional> + </when> + </conditional> + + </inputs> + + <outputs> + <data name="log" format="txt" label="CustomDataGenerator - Log" /> + + <data name="out_tabular" format="tabular" + label="${cond_model.model_selector}_data_tabular" + optional="true"/> + </outputs> <help> <![CDATA[