annotate hmmcv.xml @ 1:ef8be69b8e9e draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 108e83ea251bee3b952cb49ef758e69294608c1d

<tool id="hmmcv" name="hmmcv" version="@VERSION@">
    <description>
        HMMCV is a tool for visualization of comparisons between hidden markov models (HMM)
    </description>
   <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version" />
    <command detect_errors="aggressive"><![CDATA[
    HMMCV
        @COMMON_ARGS@
        -m $model_filepath
        -r $hmmcompare_file
    ]]></command>

    <inputs>
        <param name="model_filepath" type="data" format="hmm" label="Input model"/>
        <param name="hmmcompare_file" type="data" format="hmmcompare" 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.hmm" />
        <param name="hmmcompare_file" value="input.hmmcompare" />
        <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_1" file="Hammerhead_1.pdf" ftype="pdf" compare="sim_size" delta="50000"/>
          <element name="Hammerhead_3" file="Hammerhead_3.pdf" ftype="pdf" compare="sim_size" delta="50000" />
        </output_collection>
      </test>
    </tests>
    <help><![CDATA[ **HMMCV -- Visualisation of Hidden Markov Models comparisons**
    **Input.**
    Hidden Markov Models in HMMER3 format, comparison file in hmmcompare 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 emission probabilities and indices (simple)
    or nodes with states, emission and transition probabilities is 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>