<tool id="cmv" name="cmv" version="@VERSION@">
  <description>
    CMV is a tool for visualization of RNA family models, also known as covariance models (CM)
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  
  <expand macro="requirements" />

  <expand macro="stdio" />
  
  <expand macro="version" />
  <command><![CDATA[
  CMV
        @COMMON_ARGS@
        -m $model_filepath 
  ]]></command>
  
  <inputs>
    <param name="model_filepath" type="data" format="cm" label="Input model"/>
    <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="Hammerhead_HH9.cm" />
      <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_HH9" file="Hammerhead_HH9.pdf" ftype="pdf" compare="sim_size" />
      </output_collection>
    </test>
  </tests>
  <help><![CDATA[
  **CMV -- Visualisation of RNA family models**

  **Input.**
  Covariance Models in INFERNAL format.
  Optionally a stockholm alignment for each input model can be provided.

  **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>