<tool id="rnaalifold" name="RNAalifold" version="2.1.6.0">
    <description>Calculate minimum free energy secondary structures and partition function on a multiple alignment file</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNAalifold</token>
        <import>macros.xml</import>
    </macros>
    <command>
<![CDATA[
        RNAalifold  < $input > $tabularFile
        -T$temperature -d$dangling
        $pf
        $mis
        #if $measelect.mea=="yes"
            --mea=$measelect.meavalue
        #end if
        #if $backtrackselect.backtrack=="yes"
            --stochBT_en=$backtrackselect.backtrackvalue
        #end if
        #if $varExists('$advancedOptions.color')
            $advancedOptions.alignment
            $advancedOptions.color
            $advancedOptions.gquad
            $advancedOptions.nolp
            $advancedOptions.nogu
            $advancedOptions.noclosinggu
            $advancedOptions.notetra
            $advancedOptions.canonicalonly
            $advancedOptions.circular
            --cfactor=$advancedOptions.cfactor
            --nfactor=$advancedOptions.nfactor
            $advancedOptions.endgaps
            $advancedOptions.ribosum
        #end if
        ; tar -cf $imagesFile *.ps
]]>
    </command>
    <inputs>
        <param format="clustal" name="input" type="data" label="Clustal file"/>
        <param name="temperature" size="6" 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="0">0: ignore dangling ends</option>
            <option value="1">1: unpaired bases participate in one dangling end only</option>
            <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
            <option value="3">3: allow coaxial stacking</option>
        </param>
        <param name="pf" type="boolean" checked="false" truevalue="-p" falsevalue="" label="calculate partition function" help="-p"/>
        <param name="mis" type="boolean" checked="false" truevalue="--mis" falsevalue="" label="Most Informative Sequence" help="--mis"/>
        <conditional name="measelect">
            <param name="mea" type="select" label="calculate maximum expected accuracy" help="--MEA">
                <option value="no">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="yes">
                <param name="meavalue" size="6" type="float" value="1.0" label="Gamma Value"/>
            </when>
        </conditional>
        <conditional name="backtrackselect">
            <param name="backtrack" type="select" label="number of structures" help="--stochBT_en">
                <option value="no">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="yes">
                <param name="backtrackvalue" size="4" type="integer" value="1" label="Number of random structures."/>
            </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="alignment" type="boolean" truevalue="--aln" falsevalue="" checked="false" label="Colored and annotated alignment image" help="--color"/>
                <param name="color" type="boolean" truevalue="--color" falsevalue="" checked="false" label="Colored secondary structure image" help="--color"/>
                <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="-g  take into account G Quadruplex formation"/>
                <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="canonicalonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Canonical basepairing only" help="--canonicalBPonly"/>
                <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
                <param name="cfactor" size="6" type="float" value="1.0" label="Weight of the covariance term" help="--cfactor"/>
                <param name="nfactor" size="6" type="float" value="1.0" label="Penalty for non-compatible sequences in the covariance term" help="--nfactor"/>
                <param name="endgaps" type="boolean" truevalue="--endgaps" falsevalue="" checked="false" label="Score pairs with endgaps same as gap-gap pairs" help="--endgaps"/>
                <param name="ribosum" type="boolean" truevalue="--ribosum_scoring" falsevalue="" checked="false" label="Use ribosum scoring matrix" help="--ribosum_scoring"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="tabularFile"/>
        <data format="tar" name="imagesFile"/>
    </outputs>
    <tests>
    </tests>
    <help>
<![CDATA[
**RNAalifold**

-----

**Input format**

RNAalifold requires one input file
- Clustal file

------

**Outputs**

- energy of the consensus structures in the clustal file
- several possible postscript images bundled together in a tar file


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