<tool id="cmcv" name="CMCV" version="@VERSION@">
    <description>visualization of comparisons between RNA family models (CM)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version" />
    <command><![CDATA[
    CMCV
        @COMMON_ARGS@
        -m $model_filepath
        -r $cmcompare_file
    ]]></command>
    
    <inputs>
        <param name="model_filepath" type="data" format="cm" label="Input model"/>
        <param name="cmcompare_file" type="data" format="cmcompare" label="Input comparison"/>
        <section name="common" title="Common parameters">
            <expand macro="common_parameters" />
        </section>
    </inputs>
    <outputs>
        <expand macro="vis_output"/>
    </outputs>
    <tests>
      <test>
        <param name="model_filepath" value="hammerheadClan.cm" />
	<param name="cmcompare_file" value="input.cmcompare" />
	<param name="output_format" value="pdf" />
	<param name="model_details" value="detailed" />
	<param name="emission_layout" value="bar" />
	<output_collection name="output_pdfs" type="list">
          <element name="Hammerhead_II" file="Hammerhead_II.pdf" ftype="pdf" compare="sim_size" delta="50000"/>
	  <element name="Hammerhead_HH10" file="Hammerhead_HH10.pdf" ftype="pdf" compare="sim_size" delta="50000"/>
	</output_collection>
      </test>
    </tests>
    <help><![CDATA[
    **CMCV -- Visualisation of RNA family model comparison**

    **Input.**
    Covariance Models in INFERNAL format, comparison file in cmcompare format.

    **Output.**
    Depending on the detail level, only nodes with index (minimal), nodes with node type and indices (simple)
    or nodes with states, emission and transition probabilities are visualised. Nodes linked by input comparison data
    between different families are highlighted with color labels. 
    File in pdf,svg,png,ps format.

    For more information, see     
    .. __: https://github.com/eggzilla/cmv

    ]]></help>
    <expand macro="citations" />
</tool>