<tool id="rnaaliduplex" name="RNAaliduplex" version="2.1.6.0">
    <description>find binding sites of two RNA alignments</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNAaliduplex</token>
        <import>macros.xml</import>
    </macros>
    <command>
<![CDATA[
        RNAaliduplex -T $temperature -d $dangling $flagsort --deltaEnergy=$deltaenergy $input1 $input2
        #if $varExists('$advancedOptions.noconversion')
            $advancedOptions.noconversion
            $advancedOptions.gquad
            $advancedOptions.nolp
            $advancedOptions.nogu
            $advancedOptions.noclosinggu
            $advancedOptions.notetra
        #end if
        > $out_file
]]>
    </command>
    <inputs>
        <param format="txt" name="input1" type="data" label="Clustal alignment file"/>
        <param format="txt" name="input2" type="data" label="Clustal alignment file"/>
        <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
        <param name="deltaenergy" size="6" type="float" value="0.0" label="Compute suboptimal structures with an maximal energy difference [kcal/mol] to optimum" help="--deltaEnergy=range"/>
        <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="flagsort" type="boolean" checked="false" label="Output will be sorted by free energy" truevalue="--sorted" falsevalue="" help="--sorted"/>
        <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="noconversion" type="boolean" checked="false" truevalue="--noconv" falsevalue="" label="no conversion" help="--noconv  do not convert thymine to uracile (T -> U)."/>
                <param name="nogu" type="boolean" checked="false" truevalue="-noGU" falsevalue="" label="No GU pairing" help="--noGU  don't allow pairing of G and U."/>
                <param name="noclosinggu" type="boolean" checked="false" truevalue="--noClosingGU" falsevalue="" 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" truevalue="--noTetra" falsevalue="" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
                <param name="nolp" type="boolean" checked="false" truevalue="--noLP" falsevalue="" label="No lonely pairs (helices of length 1) will be created." help="--noLP"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="out_file"/>
    </outputs>
    <tests>
    </tests>
    <help>
<![CDATA[
**RNAaliduplex**

The program reads two alignments of RNA sequences in CLUSTAL format and
predicts optimal and suboptimal binding sites, hybridization energies and the
corresponding structures. The calculation takes only inter-molecular base pairs
into account, for the general case use RNAcofold. The use of alignments allows
to focus on binding sites that are evolutionary conserved. Note, that the two
input alignments need to have an equal number of sequences and the same order,
i.e. the 1st sequence in file1 will be hybridized to the 1st in file2 etc.

The computed binding sites, energies, and structures are written to stdout, one
structure per line. Each line consist of: The structure in dot bracket format
with a &  separating the two strands. The range of the structure in the two
sequences in the format  "from,to : from,to"; the energy of duplex structure
in kcal/mol.
The format is especially useful for computing the hybrid structure between a
small probe sequence and a long target sequence.



-----

**Input format**

RNAaliduplex takes two alignment files generated with Clustal (*.aln).

------

**Outputs**

- text output with several secondary structures and its energies

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