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<tool id="rnaup" name="RNAup" version="2.1.6.0">
    <description>Calculate the thermodynamics of RNA-RNA interactions</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNAup</token>
        <import>macros.xml</import>
    </macros>
    <command>
<![CDATA[
        RNAup < $input > $output
        -T$temperature
        --dangles=$dangling
        $constraint
        --ulength=$ulength
        --contributions=#echo ''.join(str($contributions).split(','))#
        --window=$window
        $includeboth
        $interactionpairwise
        $interactionfirst
        --extend5=$extendfive
        --extend3=$extendthree

        #if $varExists('$advancedOptions.nolp')
            --pfScale=$advancedOptions.pfscale
            $advancedOptions.noconv
            $advancedOptions.nolp
            $advancedOptions.nogu
            $advancedOptions.noclosinggu
            $advancedOptions.notetra
        #end if
        ; tar -cf $accesibilitiesFile *.out
]]>
    </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="ulength" type="integer" min="0" value="4" label="Length of the unstructured region." help="--ulength"/>
        <param name="contributions" type="select" multiple="true" display="checkboxes" label="Specify which contributions to the probabilty of being unpaired are listed in the output">
                <option value="S" selected="true">sum of all</option>
                <option value="H">unpaired within hairpin loop</option>
                <option value="I">unpaired within interior loop</option>
                <option value="M">unpaired within multiloop</option>
                <option value="E">unpaired within exterior loop</option>
                <validator type="no_options" message="Please select at least one contribution."/>
        </param>
        <param name="window" type="integer" min="0" value="25" label="Maximal length of the region of interaction." help="--window"/>
        <param name="includeboth" type="boolean" truevalue="--include_both" falsevalue="" checked="false" label="Include the probability of unpaired regions in both RNAs" help="--include_both"/>
        <param name="interactionpairwise" type="boolean" truevalue="--interaction_pairwise" falsevalue="" checked="false" label="Activate pairwise interaction mode" help="--interaction_pairwise"/>
        <param name="interactionfirst" type="boolean" truevalue="--interaction_first" falsevalue="" checked="false" label="Activate pairwise interaction mode, compare always with the first sequence" help="--interaction_first"/>
        <param name="extendfive" type="integer" min="0" value="0" label="Extend the region of interaction in the target to some residues on the 5' side." help="--extend5"/>
        <param name="extendthree" type="integer" min="0" value="0" label="Extend the region of interaction in the target to some residues on the 3' side." help="--extend3"/>

        <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="pfscale" type="float" value="1.07" label="Use scale*mfe as an estimate for the ensemble free energy " help="--pfScale"/>
                <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"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="output"/>
        <data format="tar" name="accesibilitiesFile"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="rnaup_input1.fa"/>
            <output name="output" file="rnaup_result1.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[

**RNAup**

RNAup calculates the thermodynamics of RNA−RNA interactions, by decomposing the binding into two stages. (1) First the probability that a potential binding sites remains unpaired (equivalent to the free energy needed to open the site) is computed. (2) Then this accessibility is combined with the interaction energy to obtain the total binding energy. All calculations are done by computing partition functions over all possible conformations.

RNAup provides two different modes: By default RNAup computes accessibilities, in terms of the free energies needed to open a region (default length 4). It prints the region of highest accessibility and its opening energy to stdout, opening energies for all other regions are written to a file.

In interaction mode the interaction between two RNAs is calculated. It is invoked if the input consists of two sequences concatenated with an "&". RNAup assumes that the longer RNA is a structured target sequence while the shorter one is an unstructured small RNA. Additionally, for every position along the target sequence the best free energy of binding for an interaction that includes this position is written to the the output file. Output to stdout consists of the location and free energy, dG, for the optimal region of interaction. The binding energy dG is also split into its components the interaction energy dGint and the opening energy dGu_l (and possibly dGu_s for the shorter sequence).
In addition we print the optimal interaction structure as computed by RNAduplex for this region. Note that it can happen that the RNAduplex computed optimal interaction does not coincide with the optimal RNAup region. If the two predictions don’t match the structure string is replaced by a run of ".".

-----

**Input format**

RNAup requires one input file

- Fasta file

For the interaction mode, the sequences of the query and target have to be concatenated by an '&', or the --interaction-pairwise or --interaction-first flags have to be set.

------

**Outputs**

- most accesible region of each sequence
- accesibilties of each sequence is written in a file and these files are bundled together in a tar file


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