Mercurial > repos > artbio > oases
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/oases commit d5a2de4b4c556e028fc5ef7ffcc7c2d0cf31c5ec
author | artbio |
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date | Mon, 12 Feb 2024 23:55:39 +0000 |
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ab37eb09b4ca
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/oases commit d5a2de4b4c556e028fc5ef7ffcc7c2d0cf31c5ec
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1 # 13/02/2024 |
ab37eb09b4ca
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/oases commit d5a2de4b4c556e028fc5ef7ffcc7c2d0cf31c5ec
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2 The version 1.4.0+galaxy0 of the tool uses bioconda dependencies |
ab37eb09b4ca
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/oases commit d5a2de4b4c556e028fc5ef7ffcc7c2d0cf31c5ec
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3 <requirement type="package" version="0.2.09">oases</requirement> |
ab37eb09b4ca
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/oases commit d5a2de4b4c556e028fc5ef7ffcc7c2d0cf31c5ec
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4 <requirement type="package" version="1.2.10">velvet</requirement> |
ab37eb09b4ca
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/oases commit d5a2de4b4c556e028fc5ef7ffcc7c2d0cf31c5ec
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5 <requirement type="package" version="3.12.1">python</requirement> |
ab37eb09b4ca
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/oases commit d5a2de4b4c556e028fc5ef7ffcc7c2d0cf31c5ec
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6 |
ab37eb09b4ca
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/oases commit d5a2de4b4c556e028fc5ef7ffcc7c2d0cf31c5ec
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7 |
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f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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8 # 15/04/2017 |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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9 The tool now uses bioconda dependencies |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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10 <requirement type="package" version="0.2.09">oases</requirement> |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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11 <requirement type="package" version="1.2.10">velvet</requirement> |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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12 As the output is not deterministic, test search for line matching oases locus ranging in 1-25 |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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13 |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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14 #Created 28/11/2014 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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15 #Christophe Antoniewski, CNRS/University Pierre et Marie Curie, drosofff@gmail.com |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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16 # inspired from the oases wrapper developped by Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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17 |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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18 Oases optimiser |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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19 |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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20 This Galaxy tool is intended to provide a crude but effective method of producing semi-optimised transcriptome assemblies. |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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21 It operates by performing a number of user defined Velvet assemblies upon which Oases is then run. |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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22 The results of all of these runs are then put through a final Oases step where they act as scaffolds for the main assembly. |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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23 Note that this wrapper is designed to focused on small RNA reads from small RNA sequencings and will run velvetg with kmers ranging from 11 to 35 |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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24 Prerequisites: |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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25 |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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26 1. Enclosed scripts |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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27 2. package_ged_velvet and package_ged_oases dependency packages |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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28 |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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29 Limitations: |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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30 |
f7dd852c8f4c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/oases commit 48b8101fd53263212839ecb14d3029811a3278f4
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31 This is a crude optimisation step which DOES NOT try to evaluate the quality of each assembly or map to any reference cDNA. |