comparison hyphy_gard.xml @ 25:1fb98a84e86d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"

24:4755f52427c4

<?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

            #elif str($datatype.value) == 'amino-acid':
                --model '$datatype.model'
            #end if
            #if str($rate_cond.rate):
                --rv '$rate_cond.rate'
                --rate-classes '$rate_classes'
            #end if
            --output '$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="GDD">General Discrete</option>
                <option value="Gamma">Beta-Gamma</option>
            </param>
            <when value=""/>
            <when value="GDD">
                <param argument="--rate-classes" name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
            </when>
            <when value="Gamma">
                <param argument="--rate-classes" name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
            </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"/>
        </test>
    </tests>
    <help><![CDATA[

GARD : Genetic Algorithms for Recombination Detection.

25:1fb98a84e86d

<?xml version="1.0"?>
<tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy1" 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 '$input_file' input.$input_file.extension &&
        #set $input_file = 'input.%s' % $input_file.extension

            #elif str($datatype.value) == 'amino-acid':
                --model '$datatype.model'
            #end if
            #if str($rate_cond.rate):
                --rv '$rate_cond.rate'
                --rate-classes '$rate_cond.rate_classes'
            #end if
            --output '$translated'
            --output-lf '$gard_output'
        @ERRORS@
    ]]></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="GDD">General Discrete</option>
                <option value="Gamma">Beta-Gamma</option>
            </param>
            <when value=""/>
            <when value="GDD">
                <param argument="--rate-classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
            </when>
            <when value="Gamma">
                <param argument="--rate-classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <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"/>
            <output name="translated" file="gard-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

GARD : Genetic Algorithms for Recombination Detection.