<?xml version="1.0"?>
<tool id="hyphy_strike_ambigs" name="Replace ambiguous codons" version="@TOOL_VERSION@">
    <description>in a multiple alignment using HyPhy</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        hyphy '$__tool_directory__/scripts/strike-ambigs.bf'
            --alignment '$alignment' --output '$output'
        @ERRORS@
        ]]></command>
    <inputs>
        <param name="alignment" type="data" format="fasta" label="Input alignment" />
    </inputs>
    <outputs>
        <data name="output" format="fasta" />
    </outputs>
    <tests>
        <test>
            <param name="alignment" ftype="fasta" value="strike-ambigs-in1.fa"/>
            <output name="output" file="strike-ambigs-out1.fa" />
        </test>
        <test>
            <param name="alignment" ftype="fasta" value="strike-ambigs-in2.fa"/>
            <output name="output" file="strike-ambigs-out2.fa" />
        </test>
    </tests>
    <help><![CDATA[
HyPhy Strike-Ambigs
===================

Reads an alignment of coding sequences and replaces any ambiguous codons with ---.

Note: The input fasta must be aligned along codon boundaries.
]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/bioinformatics/bti079</citation>
    </expand>
</tool>