view macros.xml @ 6:ee4be6eadd34 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit ca2d37289d712b69ac15611bbf4961d083991bba
author bgruening
date Fri, 10 Nov 2017 13:04:44 -0500
parents 6e18e0b098cd
children
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<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package">infernal</requirement>
            <requirement type="package" version="1.1.2">infernal</requirement>
            <requirement type="package" version="8.25">coreutils</requirement>
        </requirements>
    </xml>
    <token name="@VERSION@">1.1.2</token>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">@article{Nawrocki15112013,
author = {Nawrocki, Eric P. and Eddy, Sean R.},
title = {Infernal 1.1: 100-fold faster RNA homology searches},
volume = {29},
number = {22},
pages = {2933-2935},
year = {2013},
doi = {10.1093/bioinformatics/btt509},
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},
URL = {http://bioinformatics.oxfordjournals.org/content/29/22/2933.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/29/22/2933.full.pdf+html},
journal = {Bioinformatics}
}</citation>
        </citations>
    </xml>
</macros>