<tool id="viennarna_rnaplfold" name="@EXECUTABLE@" version="@VERSION@.0">
    <description> predicts RNA secondary structures including pseudoknots</description>

    <macros>
        <token name="@EXECUTABLE@">RNAplfold</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <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.noconversion
        $advancedOptions.nolp
        $advancedOptions.nogu
        $advancedOptions.noclosinggu
        $advancedOptions.notetra
    #end if
    && find -name '*_basepairs' -or -name '*_lunp' -or -name '*_openen*' > files.tmp 
    && tar -cf '$outputf' --files-from=files.tmp

]]>
    </command>

    <inputs>
        <param format="fasta" name="input" type="data" label="Fasta file"/>
        <param name="temperature" 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" 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"/>
        <param argument="--plex_output" type="boolean" truevalue="--plex_output" falsevalue="" checked="false" label="" help=""/>
        <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>
            <when value="no">
            </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="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>
        <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_collection name="matrix_outputs" type="list">                
                <element name="Anolis_caro_chrUn_GL343590.trna2-A">
                    <assert_contents>
                        <has_text_matching expression="%%Creator: ViennaRNA-@VERSION@" />
                    </assert_contents>
                </element>
            </output_collection>
        </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="citations" />
</tool>