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<tool id="rnaplfold" name="RNAplfold" version="2.1.6.0">
    <description> predicts RNA secondary structures including pseudoknots</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNAplfold</token>
        <import>macros.xml</import>
    </macros>
    <command>
<![CDATA[
        RNAplfold < $input
        -T$temperature
        --dangles=$dangling
        --cutoff=$cutoff
        --winsize=$winsize
        --span=$span
        $onthefly
        $openingenergies
        #if $varExists('$unpairedOption.ulength')
            --ulength=$unpairedOption.ulength
        #end if

        #if $varExists('$advancedOptions.nolp')
            $advancedOptions.noconv
            $advancedOptions.nolp
            $advancedOptions.nogu
            $advancedOptions.noclosinggu
            $advancedOptions.notetra
        #end if
        ;ls *_basepairs *_lunp *_openen > files.tmp
        ;tar -cf $outputf --files-from=files.tmp

]]>
    </command>

    <inputs>
        <param format="fasta" name="input" type="data" label="Fasta file"/>
        <param name="temperature" size="8" 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="2" selected="true">unpaired bases participate in all dangling ends (2)</option>
            <option value="0">ignore dangling ends (0)</option>
            <option value="1">unpaired bases participate in one dangling end only (1)</option>
            <option value="3">allow coaxial stacking (3)</option>
        </param>
        <param name="winsize" type="integer" value="70" label="Average pairing probabilities over this windowsize" help="--winsize"/>
        <param name="span" type="integer" value="70" label="Maximum seperation between base pairs" help="--span, -L"/>
        <param name="cutoff" size="8" type="float" value="0.01" label="Cutoff probability for report on base pairing" help="--cutoff"/>
        <param name="onthefly" type="boolean" truevalue="--print_onthefly" falsevalue="" checked="false" label="Print simplified base pair probabilities (_basepairs output)" help="--print_onthefly"/>
        <param name="openingenergies" type="boolean" truevalue="--opening_energies" falsevalue="" checked="false" label="Output in logarithm of the probabilities (_openen output)" help="--opening_energies"/>
        <conditional name="unpairedOption">
            <param name="unpairedSelector" type="select" label="Compute probabilty that region is unpaired (_lunp output)">
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="yes">
                <param name="ulength" type="integer" value="31" label="Maximal lenght of unpaired region" help="--ulength"/>
            </when>
        </conditional>
        <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>
        <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>
        <data format="tar" name="outputf"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="rnaplfold_input1.fa"/>
            <output name="out_file" file="rnaplfold_result1.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[

**RNAplfold**

Computes local pair probabilities for base pairs with a maximal span of L. The probabilities are averaged over all windows of size L that contain the base pair. For a sequence of length n and a window size of L the algorithm uses only O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to "scan" very large genomes for short stable RNA structures.


-----

**Input format**

RNAPplfold requires one input file

- Fasta file

------

**Outputs**

For each structure in the Fasta input a postscript image with dot-plot of the pairing probabilities is generated. Different output is generated with the "--ulength", "--print_onthefly" and "--opening_energies" flags.
The Dot Plot Matrices are stored in a Postscript file.
The other output is packed in a tar file.


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