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<tool id="rna2dfold" name="RNA2Dfold" version="2.1.6.0">
    <description>explore structure space between two reference structures</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNA2Dfold</token>
        <import>macros.xml</import>
    </macros>
    <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
        #if $varExists('$advancedOptions.noconversion')
            #if $advancedOptions.noconversion
                --noconv
            #end if
            #if $advancedOptions.nogu
                --noGU
            #end if
            #if $advancedOptions.noclosinggu
                --noClosingGU
            #end if
            #if $advancedOptions.notetra
                --noTetra
            #end if
            --maxDist1=$maxK
            --maxDist2=$maxL
        #end if
        < $custom_input > $out_file
]]>
    </command>
    <inputs>
        <param format="txt" name="custom_input" type="data" label="Custom File"/>
        <param name="temperature" size="6" 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>
            <option value="1">unpaired bases participate in one dangling end only (1)</option>
            <option value="3">allow coaxial stacking (3)</option>
        </param>
        <param name="circular" type="boolean" checked="false" label="assume circular RNA structure" help="--circ"/>
        <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" size="6" type="float" value="1.0" label="scaling factor for the partition function"/>
            </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="maxK" type="integer" value="50" label="Maximum distance to first reference structure" help="--maxDist1=INT"/>
                <param name="maxL" type="integer" value="50" label="Maximum distance to second reference structure" help="--maxDist2=INT"/>
                <param name="noconversion" type="boolean" checked="false" label="no conversion" help="--noconv  do not convert thymine to uracile (T -> U)."/>
                <param name="gquad" type="boolean" checked="false" label="G Quadruplex formation" help="-g  take into account G Quadruplex formation"/>
                <param name="nogu" type="boolean" checked="false" label="No GU pairing" help="--noGU  don't allow pairing of G and U."/>
                <param name="noclosinggu" type="boolean" 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" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" 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="requirements" />
</tool>