Mercurial > repos > tduigou > rpscore
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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
| author | tduigou |
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| date | Tue, 07 Dec 2021 15:53:15 +0000 |
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| -1:000000000000 | 0:f818d489ca7d |
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| 1 <tool id="rpscore" name="Score Pathway" version="5.9.2"> | |
| 2 <description>Computes a global score for a heterologous pathway.</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="5.9.2">rptools</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 python -m rptools.rpscore '$pathway' '$scored_pathway' | |
| 8 --no_of_rxns_thres '$adv.no_of_rxns_thres' | |
| 9 --log '$adv.log_level' | |
| 10 ]]></command> | |
| 11 <inputs> | |
| 12 <param name="pathway" type="data" format="xml" label="Pathway (rpSBML)" /> | |
| 13 <section name="adv" title="Advanced Options" expanded="false"> | |
| 14 <param name="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" /> | |
| 15 <param name="log_level" type="select" label="Log level"> | |
| 16 <option value="debug" >debug</option> | |
| 17 <option value="info" >info</option> | |
| 18 <option value="warning" >warning</option> | |
| 19 <option value="error" selected="true">error</option> | |
| 20 <option value="critical" >critical</option> | |
| 21 </param> | |
| 22 </section> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <data name="scored_pathway" format="xml" label="${tool.name} - ${pathway.name}" /> | |
| 26 </outputs> | |
| 27 <tests> | |
| 28 <test> | |
| 29 <!-- test 1: check if identical outputs are produced with default parameters --> | |
| 30 <param name="pathway" value="pathway.xml" /> | |
| 31 <output name="scored_pathway" file="scored_pathway.xml" ftype="xml" compare="diff" sort="true"/> | |
| 32 </test> | |
| 33 </tests> | |
| 34 <help><![CDATA[ | |
| 35 rpscore | |
| 36 ========= | |
| 37 | |
| 38 | |
| 39 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. | |
| 40 | |
| 41 | |
| 42 Input | |
| 43 ----- | |
| 44 | |
| 45 Required: | |
| 46 | |
| 47 * **infile**\ : (string) Pathway file (rpSBML) with scores (rules, FBA, Thermo...) | |
| 48 * **outfile**\ : (string) Path to write pathway file (rpSBML) with global score | |
| 49 | |
| 50 Advanced options: | |
| 51 | |
| 52 * **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored (too long) | |
| 53 * **--log**: (string, default=error) Set the log level, choices are 'debug', 'info', 'warning', 'error', 'critical' | |
| 54 | |
| 55 Version | |
| 56 ---------- | |
| 57 | |
| 58 5.9.2 | |
| 59 | |
| 60 Authors | |
| 61 ------- | |
| 62 | |
| 63 * **Jean-Loup Faulon** | |
| 64 * **Joan Hérisson** | |
| 65 | |
| 66 Acknowledgments | |
| 67 --------------- | |
| 68 | |
| 69 * Thomas Duigou | |
| 70 ]]></help> | |
| 71 </tool> |