<tool id="rnalalifold" name="RNALalifold" version="2.1.6.0">
    <description>Calculate locally stable secondary structures for a set of aligned RNAs</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNALalifold</token>
        <import>macros.xml</import>
    </macros>
    <command>
<![CDATA[
        RNALalifold $input > $output
        -T$temperature -d$dangling
        -L$span
        $mis

        #if $varExists('$advancedOptions.nolp')
            --cutoff=$advancedOptions.cutoff
            $advancedOptions.nolp
            $advancedOptions.nogu
            $advancedOptions.noclosinggu
            $advancedOptions.notetra
            --cfactor=$advancedOptions.cfactor
            --nfactor=$advancedOptions.nfactor
            $advancedOptions.ribosum
        #end if
        <!--; tar -cf $imagesFile *.ps -->
]]>
    </command>

    <inputs>
        <param format="clustal" name="input" type="data" label="Clustal file"/>
        <param name="span" type="integer" min="0" max="5000" value="60" label="base pair span" help="Maximal distance between two paired bases. (-L)"/>

        <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>

        <!-- the -p option led to segmentation faults with version 2.1.2 and 2.1.7 -->
        <!--<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="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="cutoff" type="float" value="0.01" label="cutoff probability for the reporting of the base pairs in the dot plot" help="--cutoff"/>
                <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="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="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="output" />
        <!-- the program does not seem to generate a dot plot, even though that is implied in the help -->
        <!--<data format="tar" name="imagesFile" label="RNALalifold images"/>-->
    </outputs>
    <tests>
    </tests>
    <help>
<![CDATA[

**RNALalifold**

Calculates locally stable RNA secondary structure with a maximal base pair span. For a sequence of length n and a base pair span of L the algorithm uses only O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to "scan" very large genomes for short RNA


-----

**Input format**

RNALalifold 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>