<macros>
    <token name="@VERSION@">1.0.8</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">cmv</requirement>
        </requirements>
    </xml>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />
        </stdio>
    </xml>

    <xml name="version">
        <version_command>
            <![CDATA[
                HMMV --version
            ]]>
        </version_command>
    </xml>

    <xml name="common_parameters">
        <param name="alignment_filepath" type="data" format="stockholm" label="Input stockholm alignment" optional="true"/>
        <param name="output_format" type="select" label="Output format" help="pdf, svg, png, ps">
            <option value="pdf">pdf</option>
            <option value="svg">svg</option>
            <option value="png">png</option>
            <option value="ps">ps</option>
        </param>
        <param name="model_details" type="select" label="Specify visualization detail level." help="minimal,simple,detailed">
            <option value="minimal">minimal</option>
            <option value="simple">simple</option>
            <option value="detailed">detailed</option>
        </param>
        <param name="emission_layout" type="select" label="Specify layout of emission probabilites." help="score,probability,bar">
            <option value="score">score</option>
            <option value="probability">probability</option>
            <option value="bar">bar</option>
        </param>
        <param argument="-t" type="float" value="0.01" label="Transition probability threshold" help="Minimal value for a transition probability to be displayed (Default: 0.01)"/>
        <param argument="-c" type="float" value="2" label="Image scaling factor" help="Set uniform scaling factor for image size (Default: 2)"/>
        <param argument="-w" type="integer" value="100" label="Maximum image width" help="Set maximal width of result figure (Default: 100)" optional="true"/>
        <param argument="-n" type="integer" value="50" label="Stockholm alignment entries"  help="Set cutoff for included stockholm alignment entries (Default: 50)" optional="true"/>
    </xml>
    
    <xml name="vis_output">
        <collection name="output_pdfs" type="list" label="${tool.name} on ${on_string}: output.pdfs">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.pdf" format="pdf"/>
            <filter>common['output_format'] == 'pdf'</filter>
        </collection>
        <collection name="output_svg" type="list" label="${tool.name} on ${on_string}: output.svgs">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.svg" format="svg"/>
            <filter>common['output_format'] == 'svg'</filter>
        </collection>
        <collection name="output_png" type="list" label="${tool.name} on ${on_string}: output.pngs">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.png" format="png"/>
            <filter>common['output_format'] == 'png'</filter>
        </collection>
        <collection name="output_ps" type="list" label="${tool.name} on ${on_string}: output.ps">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.ps" format="ps"/>
            <filter>common['output_format'] == 'ps'</filter>
        </collection>
    </xml>
    
    <token name="@COMMON_ARGS@">
      -d $common.model_details
      -e $common.emission_layout
      -n $common.n
      -w $common.w
      -c $common.c
      -t $common.t
      -f $common.output_format
      #if $common.alignment_filepath
         -s $common.alignment_filepath
      #end if 
    </token>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/nar/gkt329</citation>
        </citations>
    </xml>
</macros>