view mega_galaxy_wrapper.xml @ 0:76d433f51d11 draft default tip

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<tool id="megalaxy" name="MEGA for Galaxy" version="0.1">
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>
    <description>Galaxy interface for MEGA-CC</description>
    <command>
        <![CDATA[
            python $__tool_directory__/mega_galaxy_input.py $data_input &&
            $__tool_directory__/megacc -a $analysis_input -d mega_data.txt
            #if $advf.calibration_input
                -c $advf.calibration_input
            #end if
            #if $advf.groups_input
                -g $advf.groups_input
            #end if
            #if $advf.tree_input
                -t $advf.tree_input
            #end if
            #if $advo.format != "None"
                -f $advo.format
            #end if
            #if $advo.gap_symbol
                -gs $advo.gap_symbol
            #end if
            #if $advo.idbase_symbol
                -is $advo.idbase_symbol
            #end if
            #if $advo.missing_symbol
                -ms $advo.missing_symbol
            #end if
            -o MEGA/mega_galaxy_out 
            
        
        ]]>
    </command>

    <inputs>
        <param name="analysis_input" type="data" label="MEGA Analysis Options (.mao) File"/>
        <param name="data_input" type="data" label="Data File"/>
        <section name="advf" title="Optional Files" expanded="false">
            <param name="calibration_input" type="data" label="Calibration file" help="Provides calibration
            data for tree calling methods" optional="true"/>
            <param name="groups_input" type="data" label="Groups file"
            help="Organizes taxa into groups. Each line is a key-value pair of the form: taxonName=groupName" optional="true"/>
            <param name="tree_input" type="data" label="Tree file" help="Required for some methods" optional="true"/>
        </section>
        <section name="advo" title="Optional Arguments" expanded="false">
            <param name="concat" type="boolean" truevalue="-ca" falsevalue="" label="Concatenate Alignments"/>
            <param name="format" type="select" label="Format (for sequence alignment only)">
                <option value="None" selected="true">None</option>
                <option value="MEGA">MEGA</option>
                <option value="Fasta">Fasta</option>
            </param>
            <param name="gap_symbol" type="text" label="Gap Symbol in sequence data file" optional="true"/>
            <param name="idbase_symbol" type="text" label="Character that represents identical bases in sequence data file" optional="true"/>
            <param name="missing_symbol" type="text" label="Character that represents missing bases in sequence data file" optional="true"/>
            <param name="pfc" type="float" min="0.0" max="1.0" label="Partition Frequency Cutoff: when boostrapping, will output partition frequencies that are over given frequency" optional="true"/>
        </section>
    </inputs>
    <outputs>
        <data name="outputs" format="txt">
            <discover_datasets pattern="__designation__" directory="MEGA" visible="true" format="txt"/>
        </data>
    </outputs>
    <help>
    <![CDATA[
        Use of MEGA requires two files, a MEGA Analysis Options (.mao) file and a file with data for analysis,
        which may be one of many, including FASTA files. The MAO file must be generated prior to use of 
        MEGA. This file can be made with the MEGA prototyper, available from the `MEGA site`_. 
    
        .. _MEGA site: https://megasoftware.net
    ]]>
    </help>
    <tests>
        <test>
            <param name="analysis_input" value="infer_NJ_nucleotine.mao"/>
            <param name="data_input" value="Drosophilia_Adh.meg"/>
            <assert_stdout has_text="Analysis Complete"/>
            <assert_stdout has_text="MEGA-CC"/>
        </test>
    </tests>
</tool>