comparison hyphy_bgm.xml @ 25:d88bbb287923 draft

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

24:e14d926dfdc4

<?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 $datatype.value == "protein":
                --baseline_model '$datatype.model'
            #end if
            --branches '$branches'
            --chain '$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">

        <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_log" format="txt"/>
        <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"/>

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
            #if $datatype.value == "protein":
                --baseline_model '$datatype.model'
            #end if
            @branch_options@
            --chain '$chain_length'
            --burn_in '$burn_in'
            --samples '$samples'
            --parents '$parents'
            --min_subs '$min_subs'
        @ERRORS@
    ]]></command>
    <inputs>
        <expand macro="inputs" />
        <conditional name="datatype">
            <param name="value" type="select" label="Type of data">

        <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"/>