comparison hyphy_fubar.xml @ 26:cd41e7a4d35f draft

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

25:296409764676

<?xml version="1.0"?>
<tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@VERSION@+galaxy0" profile="19.09">
    <description>Fast Unconstrained Bayesian AppRoximation</description>
    <macros>
        <import>macros.xml</import>
        <token name="@OPERATION@">FUBAR</token>
        <token name="@operation@">fubar</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        hyphy fubar
            --alignment ./$input_file
            #if $input_nhx:
                --tree ./input.nhx
            #end if
            --code '$gencodeid'
            --method '$posteriorEstimationMethod.method'
            --grid '$grid_points'
            @posteriorEstimationMethod_cmd@
            --concentration_parameter '$concentration'
            > '$fubar_log' ;
        @CATCH_ERROR@
    ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <param argument="--grid" name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points" />
        <expand macro="conditional_posteriorEstimationMethod" />
        <param argument="--concentration_parameter" name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior" />

    </inputs>
    <outputs>
        <data name="fubar_log" format="txt"/>
        <data name="fubar_output" format="hyphy_results.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta.gz" value="fubar-in1.fa.gz"/>

26:cd41e7a4d35f

<?xml version="1.0"?>
<tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@VERSION@+galaxy1" profile="19.09">
    <description>Fast Unconstrained Bayesian AppRoximation</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        ln -s '$fubar_output' ${input_file}.FUBAR.json &&
        hyphy fubar
            --alignment ./$input_file
            @INPUT_TREE@
            --code '$gencodeid'
            --method '$posteriorEstimationMethod.method'
            --grid '$grid_points'
            @posteriorEstimationMethod_cmd@
            --concentration_parameter '$concentration'
        @ERRORS@
    ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <param argument="--grid" name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points" />
        <expand macro="conditional_posteriorEstimationMethod" />
        <param argument="--concentration_parameter" name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior" />

    </inputs>
    <outputs>
        <data name="fubar_output" format="hyphy_results.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta.gz" value="fubar-in1.fa.gz"/>