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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 044274b46d50a1d0e3708e80e0dfecf1de653c65
author | tduigou |
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date | Thu, 02 Nov 2023 14:36:09 +0000 |
parents | 241da19c48a1 |
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<tool id="rptools_rpscore" name="Score Pathway" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> <description>Computes a global score for a heterologous pathway</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ python -m rptools.rpscore '$pathway' '$scored_pathway' --no_of_rxns_thres '$adv.no_of_rxns_thres' --log "error" ]]></command> <inputs> <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" /> <section name="adv" title="Advanced Options" expanded="false"> <param argument="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" /> </section> </inputs> <outputs> <data name="scored_pathway" format="sbml" label="${tool.name} - ${pathway.name}" /> </outputs> <tests> <test> <!-- check if identical outputs are produced with default parameters --> <param name="pathway" value="pathway.xml" /> <output name="scored_pathway" file="scored_pathway.xml" ftype="sbml" compare="diff" sort="true"/> </test> </tests> <help><![CDATA[ Score Pathway ============== 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: * **Pathway (rpSBML)**\ : pathway file (rpSBML) with scores (rules, FBA, Thermo...). * **Scored pathway**\ : pathway file (rpSBML) with global score. Advanced options: * **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored ]]></help> <expand macro="creator"/> <citations> <citation type="doi">10.1038/s41467-022-32661-x</citation> </citations> </tool>