Mercurial > repos > tduigou > rpscore
view wrap.xml @ 0:f818d489ca7d draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author | tduigou |
---|---|
date | Tue, 07 Dec 2021 15:53:15 +0000 |
parents | |
children |
line wrap: on
line source
<tool id="rpscore" name="Score Pathway" version="5.9.2"> <description>Computes a global score for a heterologous pathway.</description> <requirements> <requirement type="package" version="5.9.2">rptools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python -m rptools.rpscore '$pathway' '$scored_pathway' --no_of_rxns_thres '$adv.no_of_rxns_thres' --log '$adv.log_level' ]]></command> <inputs> <param name="pathway" type="data" format="xml" label="Pathway (rpSBML)" /> <section name="adv" title="Advanced Options" expanded="false"> <param name="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" /> <param name="log_level" type="select" label="Log level"> <option value="debug" >debug</option> <option value="info" >info</option> <option value="warning" >warning</option> <option value="error" selected="true">error</option> <option value="critical" >critical</option> </param> </section> </inputs> <outputs> <data name="scored_pathway" format="xml" label="${tool.name} - ${pathway.name}" /> </outputs> <tests> <test> <!-- test 1: check if identical outputs are produced with default parameters --> <param name="pathway" value="pathway.xml" /> <output name="scored_pathway" file="scored_pathway.xml" ftype="xml" compare="diff" sort="true"/> </test> </tests> <help><![CDATA[ rpscore ========= Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, flux balance analysis and thermodynamics metrics, and the number of reactions in the pathway. Input ----- Required: * **infile**\ : (string) Pathway file (rpSBML) with scores (rules, FBA, Thermo...) * **outfile**\ : (string) Path to write pathway file (rpSBML) with global score Advanced options: * **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored (too long) * **--log**: (string, default=error) Set the log level, choices are 'debug', 'info', 'warning', 'error', 'critical' Version ---------- 5.9.2 Authors ------- * **Jean-Loup Faulon** * **Joan Hérisson** Acknowledgments --------------- * Thomas Duigou ]]></help> </tool>