comparison hyphy_bgm.xml @ 23:ede53272264e draft

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

22:373afb209788

<?xml version="1.0"?>
<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy0" 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[
        ln -s '$input_file' bgm_input.fa &&
        ln -s '$input_nhx' bgm_input.nhx &&
        hyphy bgm
            --alignment ./bgm_input.fa
            --tree ./bgm_input.nhx
            --run_type $datatype.value
            #if $datatype.value == "codon":
                --code '$datatype.gencodeid'
            #end if
            #if $datatype.value == "protein":

            --chain '$chain_length'
            --burn_in '$burn_in'
            --samples '$samples'
            --parents '$parents'
            --min_subs '$min_subs'
            > '$bgm_log'
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
        <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
        <conditional name="datatype">
            <param name="value" type="select" label="Type of data">
                <option value="nucleotide">Nucleotide</option>
                <option value="amino-acid">Amino acid</option>
                <option value="codon">Codon</option>

23:ede53272264e

<?xml version="1.0"?>
<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy0" profile="19.09">
    <description>- Detecting coevolving sites via Bayesian graphical models</description>
    <macros>
        <import>macros.xml</import>
        <token name="@OPERATION@">BGM</token>
        <token name="@operation@">bgm</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        hyphy bgm
            --alignment ./$input_file
            #if $input_nhx:
                --tree ./input.nhx
            #end if
            --run_type $datatype.value
            #if $datatype.value == "codon":
                --code '$datatype.gencodeid'
            #end if
            #if $datatype.value == "protein":

            --chain '$chain_length'
            --burn_in '$burn_in'
            --samples '$samples'
            --parents '$parents'
            --min_subs '$min_subs'
            > '$bgm_log' ;
        @CATCH_ERROR@
    ]]></command>
    <inputs>
        <expand macro="inputs" />
        <conditional name="datatype">
            <param name="value" type="select" label="Type of data">
                <option value="nucleotide">Nucleotide</option>
                <option value="amino-acid">Amino acid</option>
                <option value="codon">Codon</option>