comparison hyphy_gard.xml @ 23:a0731e81e0c2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"

22:3b96e92e8ec3

<?xml version="1.0"?>
<tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy0" profile="19.09">
    <description>Genetic Algorithm for Recombination Detection</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' gard_input.fa &&
        @HYPHYMPI@ gard
            --alignment ./gard_input.fa
            --type '$datatype.value'
            #if str($datatype.value) == 'codon':
                --code '$datatype.gencodeid'
            #elif str($datatype.value) == 'amino-acid':
                --model '$datatype.model'

            #end if
            --output '$translated'
            --output-lf '$gard_output'
            > '$gard_log'
            ;
        @CATCH_MPIERR@
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
        <conditional name="datatype">
            <param argument="--type" name="value" type="select" label="Alignment kind">
                <option value="nucleotide">Nucleotide</option>
                <option value="amino-acid">Amino acid</option>
                <option value="codon">Codon</option>

        <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 Algorithms for Recombination Detection.

23:a0731e81e0c2

<?xml version="1.0"?>
<tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy0" profile="19.09">
    <description>Genetic Algorithm for Recombination Detection</description>
    <macros>
        <import>macros.xml</import>
        <token name="@OPERATION@">GARD</token>
        <token name="@operation@">gard</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' input.$input_file.extension &&
        #set $input_file = 'input.%s' % $input_file.extension
        @HYPHYMPI@ gard
            --alignment ./$input_file
            --type '$datatype.value'
            #if str($datatype.value) == 'codon':
                --code '$datatype.gencodeid'
            #elif str($datatype.value) == 'amino-acid':
                --model '$datatype.model'

            #end if
            --output '$translated'
            --output-lf '$gard_output'
            > '$gard_log'
            ;
        @CATCH_ERROR@
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" />
        <conditional name="datatype">
            <param argument="--type" name="value" type="select" label="Alignment kind">
                <option value="nucleotide">Nucleotide</option>
                <option value="amino-acid">Amino acid</option>
                <option value="codon">Codon</option>

        <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"/>
        </test>
    </tests>
    <help><![CDATA[

GARD : Genetic Algorithms for Recombination Detection.