Mercurial > repos > tduigou > rpscore
comparison rpscore.xml @ 1:da8ae7fa5ed3 draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
| author | tduigou |
|---|---|
| date | Thu, 10 Feb 2022 12:17:38 +0000 |
| parents | |
| children | eddae32301bd |
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| 0:f818d489ca7d | 1:da8ae7fa5ed3 |
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| 1 <tool id="rpscore" name="Score Pathway" version="@TOOL_VERSION@" profile="19.09"> | |
| 2 <description>Computes a global score for a heterologous pathway.</description> | |
| 3 <macros> | |
| 4 <token name="@TOOL_VERSION@">5.12.1</token> | |
| 5 </macros> | |
| 6 <requirements> | |
| 7 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> | |
| 8 </requirements> | |
| 9 <command detect_errors="exit_code"><![CDATA[ | |
| 10 python -m rptools.rpscore '$pathway' '$scored_pathway' | |
| 11 --no_of_rxns_thres '$adv.no_of_rxns_thres' | |
| 12 --log "error" | |
| 13 ]]></command> | |
| 14 <inputs> | |
| 15 <param name="pathway" type="data" format="xml" label="Pathway (rpSBML)" /> | |
| 16 <section name="adv" title="Advanced Options" expanded="false"> | |
| 17 <param name="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" /> | |
| 18 </section> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data name="scored_pathway" format="xml" label="${tool.name} - ${pathway.name}" /> | |
| 22 </outputs> | |
| 23 <tests> | |
| 24 <test> | |
| 25 <!-- test 1: check if identical outputs are produced with default parameters --> | |
| 26 <param name="pathway" value="pathway.xml" /> | |
| 27 <output name="scored_pathway" file="scored_pathway.xml" ftype="xml" compare="diff" sort="true"/> | |
| 28 </test> | |
| 29 </tests> | |
| 30 <help><![CDATA[ | |
| 31 rpscore | |
| 32 ========= | |
| 33 | |
| 34 | |
| 35 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. | |
| 36 | |
| 37 | |
| 38 Input | |
| 39 ----- | |
| 40 | |
| 41 Required: | |
| 42 | |
| 43 * **infile**\ : (string) Pathway file (rpSBML) with scores (rules, FBA, Thermo...) | |
| 44 * **outfile**\ : (string) Path to write pathway file (rpSBML) with global score | |
| 45 | |
| 46 Advanced options: | |
| 47 | |
| 48 * **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored (too long) | |
| 49 | |
| 50 Version | |
| 51 ---------- | |
| 52 | |
| 53 5.12.1 | |
| 54 | |
| 55 Authors | |
| 56 ------- | |
| 57 | |
| 58 * **Jean-Loup Faulon** | |
| 59 * **Joan Hérisson** | |
| 60 | |
| 61 Acknowledgments | |
| 62 --------------- | |
| 63 | |
| 64 * Thomas Duigou | |
| 65 ]]></help> | |
| 66 </tool> |