comparison hyphy_bgm.xml @ 26:d1c977aee228 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2dd9bdc695433c217bbb7e11c1c0138245beb801"

25:d88bbb287923

<?xml version="1.0"?>
<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy1" profile="19.09">
    <description>- Detecting coevolving sites via Bayesian graphical models</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        hyphy bgm
            --alignment ./$input_file
            @INPUT_TREE@
            --run_type $datatype.value
            #if $datatype.value == "codon":
                --code '$datatype.gencodeid'
            #end if

        <param name="samples" type="integer" value="100" min="0" max="100" label="Number of steps to extract from chain sample"/>
        <param argument="--max-parents" name="parents" type="integer" value="1" min="1" max="3" label="Maximum number of parents allowed per node" />
        <param argument="--min-subs" name="min_subs" type="integer" value="1" min="1" max="100000" label="Minimum number of ubstitutions per site to be included in the analysis" />
    </inputs>
    <outputs>
        <data name="bgm_output" format="hyphy_results.json" from_work_dir="bgm_input.fa.BGM.json"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="bgm-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="bgm-in1.nhx"/>

26:d1c977aee228

<?xml version="1.0"?>
<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy2" profile="19.09">
    <description>- Detecting coevolving sites via Bayesian graphical models</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        ln -s '$bgm_output' ${input_file}.BGM.json &&
        hyphy bgm
            --alignment $input_file
            @INPUT_TREE@
            --run_type $datatype.value
            #if $datatype.value == "codon":
                --code '$datatype.gencodeid'
            #end if

        <param name="samples" type="integer" value="100" min="0" max="100" label="Number of steps to extract from chain sample"/>
        <param argument="--max-parents" name="parents" type="integer" value="1" min="1" max="3" label="Maximum number of parents allowed per node" />
        <param argument="--min-subs" name="min_subs" type="integer" value="1" min="1" max="100000" label="Minimum number of ubstitutions per site to be included in the analysis" />
    </inputs>
    <outputs>
        <data name="bgm_output" format="hyphy_results.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="bgm-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="bgm-in1.nhx"/>