<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">infernal</requirement>
            <requirement type="package" version="9.5">coreutils</requirement>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">1.1.5</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">infernal</xref>
        </xrefs>
    </xml>
    <xml name="DB">
        <conditional name="cm_opts">
            <param name="cm_opts_selector" type="select" label="Subject covariance models">
              <option value="db" selected="True">Locally installed covariance models</option>
              <option value="histdb">Covariance model from your history</option>
            </param>
            <when value="db">
                <param name="database" type="select" label="Covariance models">
                    <options from_data_table="infernal">
                      <column name="value" index="0"/>
                      <column name="name" index="1"/>
                      <column name="path" index="2"/>
                    </options>
                </param>
            </when>
            <when value="histdb">
                <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
            </when>
        </conditional>
    </xml>
    <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>