<tool id="rnapdist" name="RNApdist" version="2.1.6.0">
    <description>Calculate distances between thermodynamic RNA secondary structure ensembles
    </description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNApdist</token>
        <import>macros.xml</import>
    </macros>
    <command>
<![CDATA[
        RNApdist < $input > $output
        --compare=$compare
        -T$temperature -d$dangling
        $backtrack

        #if $varExists('$advancedOptions.nolp')
            $advancedOptions.noconv
            $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" size="6" 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="-d">
            <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="noconv" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion of T -> U" help="--noconv"/>
                <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" label="No lonely pairs" help="--noLP  don't allow lonely pairs."/>
                <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU  don't allow pairing of G and U."/>
                <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" label="No GU pairing at the ends" help="--noClosingGU  don't allow pairing of G and U at the ends of helices."/>
                <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
            </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="requirements" />
</tool>