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<tool id="rnasubopt" name="RNAsubopt" version="2.1.6.0">
    <description>Calculates suboptimal secondary structures of RNAs</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNAsubopt</token>
        <import>macros.xml</import>
    </macros>
    <command>
<![CDATA[
        RNAsubopt < $input > $output
        -T$temperature
        --dangles=$dangling
        #if $methodOption.methodSelector == "range"
            --deltaEnergy=$methodOption.deltaenergy
        #else
            --stochBT=$methodOption.stochastic
        #end if
        #if $outputOption.outputSelector == "yes"
            --deltaEnergyPost=$deltaenergypost
        #end if
        $constraint
        $sorted
        $dos
        $zuker
        #if $varExists('$advancedOptions.nolp')
            $advancedOptions.noconv
            $advancedOptions.nolp
            $advancedOptions.nogu
            $advancedOptions.noclosinggu
            $advancedOptions.notetra
            $advancedOptions.logml
        #end if
]]>
    </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="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Constraints for the secondary structure" help="--constraint"/>
        <param name="sorted" type="boolean" truevalue="--sorted" falsevalue="" checked="false" label="Sort the secondary structures by energy" help="--sorted"/>
        <param name="dos" type="boolean" truevalue="--dos" falsevalue="" checked="false" label="Calculate the density of states instead of the structure" help="--dos"/>
        <param name="zuker" type="boolean" truevalue="--zuker" falsevalue="" checked="false" label="Calculate the Zuker suboptimals instead of the structures within a range." help="--zuker"/>

        <conditional name="methodOption">
            <param name="methodSelector" type="select" label="select algorithm">
                <option value="range" selected="true">energy range</option>
                <option value="stochastic">choose stochastically</option>
            </param>
            <when value="stochastic">
                <param name="stochastic"  type="integer" value="1" label="Calculate this number of suboptimal structures chosen stochastically" help="--stochBT"/>
            </when>
            <when value="range">
                <param name="deltaenergy" size="8" type="float" value="1.0" label="Range of energy for the suboptimal structures." help="--deltaEnergy"/>
            </when>
        </conditional>

        <conditional name="outputOption">
            <param name="outputSelector" type="select" label="select output restriction">
                <option value="no" selected="true">no restriction</option>
                <option value="yes">restricted output</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param name="deltaenergypost" size="8" type="float" value="0.0" label="Print only those structures that have a smaller difference in energy than the mfe." help="--deltaEnergyPost"/>
            </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="circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
                <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"/>
                <param name="logml" type="boolean" truevalue="--logML" falsevalue="" checked="false" label="Recalculate energies of structures using a logarithmic energy function for multi-loops" help="--logML"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="output"/>
    </outputs>
    <tests>
    </tests>
    <help>
<![CDATA[

**RNAsubopt**

In the default -e mode RNAsubopt calculates all suboptimal secondary structures within a user defined energy range above the minimum free energy (mfe). It prints the suboptimal structures in dot-bracket notation followed by the energy in kcal/mol to stdout. Be careful, the number of structures returned grows exponentially with both sequence length and energy range.

Alternatively, when used with the -p option, RNAsubopt produces Boltzmann weighted samples of secondary structures.


-----

**Input format**

RNAsubopt requires one input file

- fasta file


------

**Outputs**

- secondary structure in dot-bracket format


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