<tool id="funannotate_sort" name="Sort assembly" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools" />
    <requirements>
        <expand macro="requirements" />
    </requirements>
    <version_command>funannotate check --show-versions</version_command>
    <command><![CDATA[
funannotate sort
--input '${input}'
--out '${output}'
--base '${base}'
--minlen ${minlen}
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="fasta" label="Assembly to sort" />

        <param argument="--base" type="text" value="scaffold" label="Base name to relabel contigs">
            <validator type="regex" message="No special characters allowed">^(?:\w+)?$</validator>
        </param>
        <param argument="--minlen" type="integer" value="0" label="Shorter contigs are discarded" />
    </inputs>
    <outputs>
        <data name='output' format='fasta' label="${tool.name} on ${on_string}: sorted assembly" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="genome.fa" />
            <output name="output">
                <assert_contents>
                    <has_text text=">scaffold_1" />
                    <has_text text=">scaffold_4" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="genome.fa" />
            <param name="base" value="something" />
            <param name="minlen" value="2100" />
            <output name="output">
                <assert_contents>
                    <has_text text=">something_1" />
                    <not_has_text text=">something_4" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Funannotate_ sort
-----------------

Funannotate_ is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).

This script sorts the input contigs by size (longest->shortest) and then relabels
the contigs with a simple name (e.g. scaffold_1).  Augustus can have problems with
some complicated contig names.

.. _Funannotate: http://funannotate.readthedocs.io
    ]]></help>
    <expand macro="citations" />
</tool>