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author | tduigou |
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date | Tue, 07 Dec 2021 15:53:15 +0000 |
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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> |