Mercurial > repos > bimib > marea_2
changeset 89:5ea689ae9eac draft
Uploaded
author | luca_milaz |
---|---|
date | Sat, 20 Jul 2024 16:07:22 +0000 |
parents | ae7c31133059 |
children | 04e8b86d4366 |
files | marea_2/ras_to_bounds.xml |
diffstat | 1 files changed, 79 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/marea_2/ras_to_bounds.xml Sat Jul 20 16:07:22 2024 +0000 @@ -0,0 +1,79 @@ +<tool id="MaREA RAS to bounds" name="RAStoBounds" 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__/ras_to_bounds.py + --model_selector $cond_model.model_selector + #if $cond_model.model_selector == 'Custom' + --model $model + --model_name $model.element_identifier + #end if + --medium_selector $cond_medium.medium_selector + #if $cond_medium.medium_selector == 'Custom' + --medium $medium + --medium_name $medium.element_identifier + #end if + --input_ras $input_ras + --out_log $log + ]]> + </command> + <inputs> + <conditional name="cond_model"> + <expand macro="options_ras_to_bounds_model"/> + <when value="Custom"> + <param name="model" argument="--model" type="data" format="json, xml" label="Custom model" /> + </when> + </conditional> + + <param name="input_ras" argument="--input_ras" multiple="false" type="data" format="tabular, csv, tsv" label="RAS matrix:" /> + + <conditional name="cond_medium"> + <expand macro="options_ras_to_bounds_medium"/> + <when value="Custom"> + <param name="medium" argument="--medium" type="data" format="csv" label="Custom medium" /> + </when> + </conditional> + + </inputs> + + <outputs> + <data format="txt" name="log" label="RAStoBounds - $name - Log" /> + + <collection name="results" type="list" label="Ras to Bounds ($output_format)"> + <discover_datasets name = "collection" pattern="__name_and_ext__" directory="result"/> + </collection> + </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> \ No newline at end of file