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

    <macros>
        <token name="@EXECUTABLE@">RNAPKplex</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
    RNAPKplex < '$input' > '$output'
    -T$temperature
    --energyCutoff=$energycutoff
    #if $varExists('$advancedOptions.nolp')
        --cutoff=$advancedOptions.cutoff
        --subopts=$advancedOptions.suboptimal
        $advancedOptions.verbose
        $advancedOptions.noconversion
        $advancedOptions.nolp
        $advancedOptions.nogu
        $advancedOptions.noclosinggu
        $advancedOptions.notetra
    #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="energycutoff" type="float" value="-8.1" label="Pseudoknots cutoff. Pseudoknots with smaller energy gains are rejected." help="--energyCutoff"/>
        <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="suboptimal" type="float" value="0.0" label="Print suboptimal pseudoknots" help="--subopts"/>
                <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Verbose mode, more output" help="--verbose"/>
                <param name="cutoff" type="float" value="0.01" label="cutoff probability for the reporting of the base pairs in the dot plot" help="--cutoff"/>
                <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"/>
        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.ps" ext="eps" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="rnapkplex_input1.fa"/>
            <output name="out_file" file="rnapkplex_result1.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[

**RNAPKplex**

Computes RNA secondary structures by first making two sequence intervals accessible and unpaired using the algorithm of RNAplfold and then calculating the energy of the interaction of those two intervals. The algorithm uses O(n^2*w^4) CPU time and O(n*w^2) memory space. The algorithm furthermore always considers dangle=2 model.

It also produces a PostScript file with a plot of the pseudoknot-free secondary structure graph, in which the bases forming the pseuodknot are marked red.

For each structure in the Fasta input, a PostScript file is produced for the structure graph.

-----

**Input format**

RNAPKplex requires one input file

- fasta file

The input format is similar to fasta except that even long sequences may not be interrupted by line breaks, and the header lines are optional.

------

**Outputs**

- secondary structure in dot-bracket format
- Images of the calculated structures

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