Mercurial > repos > tduigou > rpscore
diff wrap.xml @ 0:f818d489ca7d draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author | tduigou |
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date | Tue, 07 Dec 2021 15:53:15 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wrap.xml Tue Dec 07 15:53:15 2021 +0000 @@ -0,0 +1,71 @@ +<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> \ No newline at end of file