<tool id="rnacofold" name="RNAcofold" version="2.1.6.0">
    <description>Calculate secondary structures of two RNAs with dimerization</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNAcofold</token>
        <import>macros.xml</import>
    </macros>
    <command>
<![CDATA[
        RNAcofold  < $input > $tabularFile
        -T$temperature -d$dangling
        $pf
        $allpf
        #if $varExists('$advancedOptions.noconversion')
            $advancedOptions.constraint
            $advancedOptions.noconversion
            $advancedOptions.gquad
            $advancedOptions.nolp
            $advancedOptions.nogu
            $advancedOptions.noclosinggu
            $advancedOptions.notetra
        #end if
]]>
    </command>
    <inputs>
        <param format="fasta" name="input" type="data" label="Fasta 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="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
        <param name="allpf" type="boolean" checked="false" truevalue="--all_pf" falsevalue="" label="Calculate homo-dimers" help="--all_pf"/>
        <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="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate structure subject to constraints" help="--constraint"/>
                <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion T->U" help="--noconv"/>
                <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"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="tabularFile"/>
        <collection name="sequence_outputs" type="list" label="rna_eps outputs">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" />
        </collection>
        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
            <filter>pf is True</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
        </collection>
    </outputs>
    <tests>
    </tests>
    <help>
<![CDATA[
**RNAcofold**


-----

**Input format**

RNAcofold requires one input file:

- Fasta file

Two different RNA sequences can be specified concatenated with the '&' character. The folding of the two sequences with each other will be calculated.


------

**Outputs**

- Energies of the RNA sequences and the dimers
- Structure images
- Dot Plot Matrix images (if --partfunc is used)

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