<tool id="viennarna_rna2dfold" name="@EXECUTABLE@" version="@VERSION@.0">
    <description>explore structure space between two reference structures</description>
    <macros>
        <token name="@EXECUTABLE@">RNA2Dfold</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        RNA2Dfold -T $temperature -d $dangling --stochBT=$nrbt
        #if int($nk) > -1 and int($nl) > -1
            --neighborhood=$nk:$nl
        #end if
        #if $varExists('$pfselect.pfscaling')
            --partfunc --pfScale=$pfselect.pfscaling
        #end if
        $noBT
        $advancedOptions.noconversion
        $advancedOptions.noclosinggu
        $advancedOptions.notetra
        $advancedOptions.circ
        #if $varExists('$advancedOptions.maxK')    
            --maxDist1=$advancedOptions.maxK
            --maxDist2=$advancedOptions.maxL
        #end if
        < '$custom_input' > '$out_file'
]]>
    </command>
    <inputs>
        <param format="txt,dbn" name="custom_input" type="data" label="Custom File"/>
        <param name="temperature" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
        <param name="nrbt" type="integer" value="1" label="Number of backtrack of Boltzmann samples" help="--stochBT=INT"/>
        <param name="nk" type="integer" value="-1" label="[k]: Distance to first reference structure of neighborhood in which to backtrack" help="--neighborhood=k:l"/>
        <param name="nl" type="integer" value="-1" label="[l]: Distance to second reference structure of neighborhood in which to backtrack" help="--neighborhood=k:l"/>
        <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>
        </param>
        <param name="noBT" type="boolean" checked="true" truevalue="" falsevalue="--noBT" 
            label="Backtrack structures, don't calculate energy contributions only" argument="--noBT"/>
        <conditional name="pfselect">
            <param name="pf" type="select" label="Calculate partition function" help="--partfunc">
                <option value="no">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="yes">
                <param name="pfscaling" type="float" value="1.0" label="Scaling factor for the partition function"/>
            </when>
            <when value="no">
            </when>
        </conditional>
        <section name="advancedOptions" title="Advanced options">
            <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="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>
            <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 argument="--circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Model as circular RNA structure"/>                                      
            <param name="maxK" type="integer" value="10" max="44" label="Maximum distance to first reference structure" argument="--maxDist1"/>
            <param name="maxL" type="integer" value="10" max="43" label="Maximum distance to second reference structure" argument="--maxDist2"/>
            <!-- This argument causes "Segmentation fault"-->
            <!-- <param name="nogu" type="boolean" truevalue="" falsevalue="- -noGU" checked="true" label="Allow GU pairing" help="Allow wobbly pairs G-U."/> -->               
        </section>
    </inputs>
    <outputs>
        <data format="dbn" name="out_file"/>
    </outputs>
    <tests>
        <test>
            <param name="custom_input" value="rna2dfold_input1.txt"/>
            <param name="nrbt" value="0"/>
            <output name="out_file1" file="rna2dfold_result1.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[
**RNA2Dfold**

The program partitions the secondary structure space into (basepair)distance
classes according to two fixed reference structures. It expects a sequence and
two secondary structures in dot-bracket notation as its inputs. For each
distance class, the MFE representative, Boltzmann probabilities and Gibbs free
energy is computed. Additionally, a stochastic backtracking routine allows to
produce samples of representative suboptimal secondary structures from each
partition.
The k-distance corresponds to the distance to the first reference structure, and
the l-distance corresponds to the distance to the second reference structure

-----

**Input format**

RNA2Dfold requires one input file in the following format

- 1st line: RNA sequence
- 2nd line: first reference structure in dot-bracket format
- 3rd line: second reference structure in dot-bracket format

------

**Outputs**

- text output with several secondary structures and its energies

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