<tool id="viennarna_rnadpdist" name="@EXECUTABLE@" version="@VERSION@.0">
    <description>Calculate distances between thermodynamic RNA secondary structure ensembles
    </description>

    <macros>
        <token name="@EXECUTABLE@">RNApdist</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
    RNApdist < '$input' > '$output'
    --compare=$compare
    -T$temperature -d$dangling
    $backtrack
    #if $varExists('$advancedOptions.nolp')
        $advancedOptions.noconversion
        $advancedOptions.nolp
        $advancedOptions.nogu
        $advancedOptions.noclosinggu
        $advancedOptions.notetra
    #end if
    #if $backtrack and str($compare)=="m"
        && cat backtrack.file >> '$outfile'
    #end if

]]>
    </command>

    <inputs>
        <param format="fasta" name="input" type="data" label="Fasta file"/>
        <param name="temperature" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
        <param name="dangling" type="select" label="How to treat dangling end energies" help="-d">
            <option value="0">0: ignore dangling ends</option>
            <option value="1">1: unpaired bases participate in one dangling end only</option>
            <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
            <option value="3">3: allow coaxial stacking</option>
        </param>
        <param name="compare" type="select" label="Comparison Option" help="--compare">
            <option value="p" selected="True">p: pairwise (1st with 2nd, 3rd with 4th, ...)</option>
            <option value="m">m: matrix (each with each, output in matrix form)</option>
            <option value="f" >f: first (1st with 2nd, 1st with 3rd, ...)</option>
            <option value="c">c: continuous (1st with 2nd, 2nd with 3rd, ...)</option>
        </param>
        <param name="backtrack" type="boolean" checked="false" truevalue="--backtrack" falsevalue="" label="Print an alignment" help="--backtrack"/>
        <conditional name="advancedOptions">
            <param name="advancedSelector" type="select" label="advanced options">
                <option value="basic">basic Options</option>
                <option value="advanced">advanced Options</option>
            </param>
            <when value="advanced">
                <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
                <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
                <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/>
                <param name="notetra" type="boolean" truevalue="" falsevalue="--noTetra" checked="true" label="Allow stabilization for loops, hairpins etc." help=" Include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (--noTetra)"/>
                <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>
            </when>
            <when value="basic">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="output"/>
        <data format="txt" name="dotplot"/>
        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="rnapdist_input1.fa"/>
            <output name="out_file" file="rnapdist_result1.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[

**RNApdist**

RNApdist calculates structure distances between the thermodynamic ensembles of the secondary structures of RNA sequences.

-----

**Input format**

RNApdist requires one input file
- Fasta file

------

**Outputs**

- output of alignment scores and alignments (if -B option is selected)
- dot plot matrices in postscript format bundled together in a tar file

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