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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
author bgruening
date Thu, 23 Sep 2021 19:38:58 +0000
parents ee4be6eadd34
children
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6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package">infernal</requirement>
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5 <requirement type="package" version="1.1.4">infernal</requirement>
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6 <requirement type="package" version="8.32">coreutils</requirement>
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7 </requirements>
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8 </xml>
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9 <token name="@TOOL_VERSION@">1.1.4</token>
c9e29ac5d099 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
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10 <token name="@VERSION_SUFFIX@">0</token>
c9e29ac5d099 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
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11 <xml name="xrefs">
c9e29ac5d099 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
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12 <xrefs>
c9e29ac5d099 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
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13 <xref type="bio.tools">infernal</xref>
c9e29ac5d099 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
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14 </xrefs>
c9e29ac5d099 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
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15 </xml>
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16 <xml name="stdio">
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17 <stdio>
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18 <exit_code range="1:" />
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19 <exit_code range=":-1" />
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20 <regex match="Error:" />
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21 <regex match="Exception:" />
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22 </stdio>
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23 </xml>
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24 <xml name="citations">
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25 <citations>
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26 <citation type="bibtex">@article{Nawrocki15112013,
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27 author = {Nawrocki, Eric P. and Eddy, Sean R.},
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28 title = {Infernal 1.1: 100-fold faster RNA homology searches},
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29 volume = {29},
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30 number = {22},
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31 pages = {2933-2935},
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32 year = {2013},
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33 doi = {10.1093/bioinformatics/btt509},
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34 abstract ={Summary: Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input. Infernal uses CMs to search for new family members in sequence databases and to create potentially large multiple sequence alignments. Version 1.1 of Infernal introduces a new filter pipeline for RNA homology search based on accelerated profile hidden Markov model (HMM) methods and HMM-banded CM alignment methods. This enables ∼100-fold acceleration over the previous version and ∼10 000-fold acceleration over exhaustive non-filtered CM searches.Availability: Source code, documentation and the benchmark are downloadable from http://infernal.janelia.org. Infernal is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X. Documentation includes a user’s guide with a tutorial, a discussion of file formats and user options and additional details on methods implemented in the software.Contact: nawrockie@janelia.hhmi.org},
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35 URL = {http://bioinformatics.oxfordjournals.org/content/29/22/2933.abstract},
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36 eprint = {http://bioinformatics.oxfordjournals.org/content/29/22/2933.full.pdf+html},
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37 journal = {Bioinformatics}
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38 }</citation>
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39 </citations>
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40 </xml>
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41 </macros>