annotate hmmv.xml @ 0:159092b83639 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c

<tool id="hmmv" name="hmmv" version="@VERSION@.1">
    <description>
        HMMV is a tool for visualization of hidden markov models (HMM)
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version" />
    <command detect_errors="aggressive"><![CDATA[
    HMMV
        @COMMON_ARGS@
        -m '$model_filepath'
    ]]></command>
    <inputs>
         <param name="model_filepath" type="data" format="hmm3" 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="tRNA.hmm" />
            <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="tRNA" file="tRNA.pdf" ftype="pdf" compare="sim_size" delta="50000" />
            </output_collection>
        </test>
    </tests>
        <help><![CDATA[ **HMMV -- Visualisation of Hidden Markov Models**
    **Input.**
    Hidden Markov Models in HMMER3 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.
    File in pdf,svg,png,ps format.
    
    For more information, see     
    .. __: https://github.com/eggzilla/cmv
    ]]>
    </help>
    <expand macro="citations" />
</tool>