<?xml version="1.0"?>
<tool id="hyphy_conv" name="HyPhy-Conv" version="@VERSION@+galaxy1" profile="19.09">
    <description>translate an in-frame codon alignment to proteins</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        cp '$input_file' conv_input.fa &&
        hyphy conv
            '$gencodeid'
            '$deletions'
            conv_input.fa
            aa.nex
        @ERRORS@
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fasta" label="Input codon alignment"/>
        <expand macro="gencode"/>
        <param name="deletions" type="boolean" truevalue="Keep Deletions" falsevalue="Skip Deletions" label="Keep deletions" help="If this is checked, deletions will be left in the output file"/>
    </inputs>
    <outputs>
        <data name="proteins" format="nex" from_work_dir="aa.nex" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="conv-in1.fa"/>
            <param name="deletions" value="Keep Deletions" />
            <output name="proteins" file="conv-out1.nex" />
        </test>
    </tests>
    <help><![CDATA[
HyPhy-CONV: Translate an in-frame codon alignment to proteins
=============================================================

This tool takes a codon-aligned fasta file and outputs the amino acid sequence
it represents, with the option to keep or skip deletions in the input file.
]]>
    </help>
    <expand macro="citations" />
</tool>