<tool id="aligned_to_consensus" name="Consensus sequence from aligned FASTA" version="@VERSION@">
    <description></description>
    <macros>
        <import>consalign_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="0.1.4">r-bioseq</requirement>
        <requirement type="package" version="1.0.14">r-ptxqc</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript
         '$__tool_directory__/consensus_from_alignments.R'
         '$input'
         '$seqtype'
         '$method'
         '$gaps'
         '$outog'
         '$output'
    ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="fasta" label="Input fasta file with at least two sequences"/>
        <param name="seqtype" type="select" label="Type of sequence" multiple="false" optional="false" display="radio">
            <option value="DNA" selected="true">DNA</option>
            <option value="RNA">RNA</option>
            <option value="AA">Amino Acid</option>
        </param>
        <param name="method" type="select" label="Consensus method when differences are found between sequences" multiple="false" optional="false" display="radio">
            <option value="chr_ambiguity" selected="true">Use an ambiguous nucleotide</option>
            <option value="chr_majority">Use the most frequent nucleotide</option>
        </param>
        <param name="gaps" type="boolean" checked="no" label="Take account of gaps?" help="/!\ If gaps are at the same place in all the sequences don't check 'no', you'll face an error"/>
        <param name="outog" type="boolean" checked="no" label="Output consensus sequence AND original sequences in the FASTA file?" help="/!\ If gaps are at the same place in all the sequences don't check 'no', you'll face an error"/>
    </inputs>
    <outputs>
        <data name="output" from_work_dir="output.fasta" format="fasta" label="Consensus sequence of ${input.display_name}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="test_file.fasta"/>
            <param name="seqtype" value="DNA"/>
            <param name="method" value="chr_ambiguity"/>
            <param name="gaps" value="false"/>
            <param name="outog" value="false"/>
            <output name="output">
                <assert_contents> 
                    <has_n_lines n="2"/>
                </assert_contents> 
            </output>
        </test>
    </tests>
    <help><![CDATA[
=====================================================
Get consensus sequence from several aligned sequences
=====================================================

This tool uses the seq_consensus function from the bioseq package. @WARNING@ If gaps are at the same place in all the sequences don't check 'no' in the gaps parameter,
you'll face an error.

Input can be any fasta file containing at least two aligned sequences.

Output is a FASTA file containing the computed consensus sequence (along with original sequences if you want to).
    ]]></help>
    <citations>
        <citation type="doi">10.1111/2041-210X.13490</citation>
    </citations>
</tool>