comparison hyphy_gard.xml @ 1:a03d87763f51 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"

0:1942d02039c2

            #end if
            --rv '$rate_cond.rate'
            #if str($rate_cond.rate) != 'None':
                --rate-classes '$rate_classes'
            #end if
            > '$gard_log'
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
        <conditional name="datatype">
            <param name="value" type="select" label="Type of data">
                <option value="Nucleotide">Nucleotide</option>
                <option value="Protein">Amino acid</option>
                <option value="Codon">Codon</option>
            </param>
            <when value="Nucleotide"/>
            <when value="Protein">
                <expand macro="substitution" />
            </when>

            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="gard_log" format="txt"/>
        <data name="gard_output" format="nex" from_work_dir="gard_input.GARD_finalout"/>
        <data name="translated" format="hyphy_results.json" from_work_dir="gard_input.fa.json"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="gard-in1.fa"/>
            <output name="gard_output" file="gard-out1.nex" compare="sim_size" delta="160000"/>
        </test>
    </tests>
    <help><![CDATA[
GARD (Genetic Algorithm for Recombination Detection) is a method to screen a multiple sequence analysis for the presence of recombination and is extremely useful as a pre-processing step for selection inference. Because recombinant sequences cannot be adequately described with a single phylogenetic history, selection inference on recombinant data often leads to a significant increase in false positives. GARD alleviates this concern by comprehensively screening an alignment for recombination breakpoints and inferring a unique phylogenetic history for each detected recombination block.
    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msl051</citation>
    </expand>
</tool>

1:a03d87763f51

            #end if
            --rv '$rate_cond.rate'
            #if str($rate_cond.rate) != 'None':
                --rate-classes '$rate_classes'
            #end if
            --output '$translated'
            --output-lf '$gard_output'
            > '$gard_log'
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
        <conditional name="datatype">
            <param name="value" type="select" label="Type of data">
                <option value="nucleotide">Nucleotide</option>
                <option value="protein">Amino acid</option>
                <option value="codon">Codon</option>
            </param>
            <when value="Nucleotide"/>
            <when value="Protein">
                <expand macro="substitution" />
            </when>

            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="gard_log" format="txt"/>
        <data name="gard_output" format="nex" />
        <data name="translated" format="hyphy_results.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="gard-in1.fa"/>
            <output name="gard_output" file="gard-out1.nex" compare="sim_size" delta="160000"/>
        </test>
    </tests>
    <help><![CDATA[
GARD (Genetic Algorithm for Recombination Detection) is a method to screen a multiple sequence analysis for the presence of recombination and is extremely useful as a pre-processing step for selection inference. Because recombinant sequences cannot be adequately described with a single phylogenetic history, selection inference on recombinant data often leads to a significant increase in false positives. GARD alleviates this concern by comprehensively screening an alignment for recombination breakpoints and inferring a unique phylogenetic history for each detected recombination block.

See the online documentation_ for more information.

.. _documentation: http://hyphy.org/methods/selection-methods/#gard
    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msl051</citation>
    </expand>
</tool>