<tool id="raptor-search" name="raptor search" version="2.0.0+8" python_template_version="3.5">
    <description>
        Queries an index to determine which fasta file the query can be found in.
    </description>
    <requirements>
        <requirement type="package" version="2.0.0">raptor</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '${query}' query.fasta;
        raptor search
            --index '${index}'
            --query query.fasta
            --output results.txt
            #if $threshold# --threshold ${threshold} #end if#
            #if $tau#       --tau ${tau} #end if#
            #if $pattern#   --pattern ${pattern} #end if#
    ]]></command>
    <inputs>
        <param name="threads" label="Threads" type="integer" value="1" min="1" help="The numer of threads to use. Default: 1. Value must be a positive integer." />
        <param name="index" label="Index" type="data" format="binary" help="Provide a valid path to an index. Parts: Without suffix _0 " />
        <param name="query" label="Query" type="data" format="fasta" help="Provide a path to the query file. The input file must exist and read permissions must be granted." />
        <param name="error" label="Allowed errors" type="integer" value="0" min="0" help="The number of errors Default: 0. Value must be a positive integer or 0." />
        <param name="tau" label="Probabilistic threshold τ" type="float" value="0.99" min="0" max="1" help="Threshold for probabilistic models. Default: 0.99. Value must be in range [0,1]." />
        <param name="threshold" label="Non-Probabilistic threshold" type="float" value="0" min="0" max="1" optional="true" help="If set, this threshold is used instead of the probabilistic models. Default: 0. Value must be in range [0,1]." />
        <param name="pattern" label="Pattern size" type="integer" optional="true" help="The pattern size. Default: Use median of sequence lengths in query file. Default: 0." />
    </inputs>
    <outputs>
        <data name="results" format="txt" from_work_dir="results.txt" />
    </outputs>
    <tests>
        <test>
            <param name="index" value="test_expected.index" />
            <param name="query" value="query.fasta" />
            <output name="results" file="expected_query_results.txt" />
        </test>
    </tests>
    <help><![CDATA[Raptor - A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.
===========================================================================================================

OPTIONS

  Basic options:
    --threads (unsigned 8 bit integer)
          The numer of threads to use. Default: 1. Value must be a positive integer.
    --index (std::filesystem::path)
          Provide a valid path to an index. Parts: Without suffix _0
    --query (std::filesystem::path)
          Provide a path to the query file. The input file must exist and read permissions must be granted.
    --output (std::filesystem::path)
          Provide a path to the output.
    --error (unsigned 8 bit integer)
          The number of errors Default: 0. Value must be a positive integer or 0.
    --tau (double)
          Threshold for probabilistic models. Default: 0.99. Value must be in range [0,1].
    --threshold (double)
          If set, this threshold is used instead of the probabilistic models. Default: 0. Value must be in range
          [0,1].
    --pattern (unsigned 64 bit integer)
          The pattern size. Default: Use median of sequence lengths in query file. Default: 0.

EXAMPLES
    raptor search --error 2 --index raptor.index --query queries.fastq --output search.output

VERSION
    Last update: 2021-08-26
    Raptor version: 2.0.0 (raptor-v2.0.0)
    SeqAn version: 3.1.0-rc.2

URL
    https://github.com/seqan/raptor

LEGAL
    Raptor Copyright: BSD 3-Clause License
    Author: Enrico Seiler
    Contact: enrico.seiler@fu-berlin.de
    SeqAn Copyright: 2006-2021 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
    In your academic works please cite: Raptor: A fast and space-efficient pre-filter for querying very large
    collections of nucleotide sequences; Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, and Knut
    Reinert; iScience 2021 24 (7): 102782. doi: https://doi.org/10.1016/j.isci.2021.102782
    For full copyright and/or warranty information see --copyright.
    ]]></help>
    <citations>
        <citation type="bibtex">
@Article{Seiler2021,
author={Seiler, Enrico
and Mehringer, Svenja
and Darvish, Mitra
and Turc, Etienne
and Reinert, Knut},
title={Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences},
journal={iScience},
year={2021},
month={Jul},
day={23},
publisher={Elsevier},
volume={24},
number={7},
issn={2589-0042},
doi={10.1016/j.isci.2021.102782},
url={https://doi.org/10.1016/j.isci.2021.102782}
}</citation>
    </citations>
</tool>