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<tool id="rnaplex" name="RNAplex" version="2.1.6.0">
    <description>Find targets of a query RNA</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNAplex</token>
        <import>macros.xml</import>
    </macros>
    <command>
<![CDATA[
        RNAplex
        #if str($clustalOption.clustalFlag) == "clustal"
            --alignment-mode
            -q$input1 -t$input2
        #else
            < $input
        #end if
        -T$temperature
        --interaction-length=$maxLength
        --extension-cost=$extensionCost
        --scale-accessibility=$scaleAccessibility
        $constraint


        #if $varExists('clustalOption.meltingOption.probeConc')
            --probe-mode
            --probe-concentration=$clustalOption.meltingOption.probeConc
            --na-concentration=$clustalOption.meltingOption.naConc
            --mg-concentration=$clustalOption.meltingOption.mgConc
            --k-concentration=$clustalOption.meltingOption.kConc
            --tris-concentration=$clustalOption.meltingOption.trisConc
        #end if



        #if $varExists('$advancedOptions.duplexDistance')
            --fast-folding=$advancedOptions.fastFolding
            --duplex-distance=$advancedOptions.duplexDistance
            --energy-threshold=$advancedOptions.enThreshold
        #end if
        > $output
]]>
    </command>

    <inputs>
    <conditional name="clustalOption">
        <param name="clustalFlag" type="select" label="Input options">
            <option value="fasta" selected="true">Fasta input file</option>
            <option value="clustal">Clustalw input files</option>
        </param>
        <when value="fasta">
            <param format="fasta" name="input" type="data" label="Fasta file"/>
            <conditional name="meltingOption">
                <param name="meltingSelector" type="select" label="calculate melting temperature">
                    <option value="no" selected="true">no</option>
                    <option value="yes">yes</option>
                </param>
                <when value="yes">
                    <param name="probeConc" type="float" value="0.1" label="Concentration of the probe" help="--probe-concentration"/>
                    <param name="naConc" type="float" value="1.0" label="Na concentration" help="--na-concentration"/>
                    <param name="mgConc" type="float" value="1.0" label="Mg concentration" help="--mg-concentration"/>
                    <param name="kConc" type="float" value="1.0" label="K concentration" help="--k-concentration"/>
                    <param name="trisConc" type="float" value="1.0" label="Tris concentration" help="--tris-concentration"/>
                </when>
            </conditional>
            </when>
        <when value="clustal">
            <param format="txt" name="input1" type="data" label="Clustal file / Query sequences"/>
            <param format="txt" name="input2" type="data" label="Clustal file / Target sequences"/>
        </when>
    </conditional>
        <param name="temperature" size="8" type="float" value="37.0" label="temperature [°C]" help="-T"/>
        <param name="maxLength" type="integer" min="0" value="40" label="maximal interaction length" help="--interaction-length"/>
        <param name="extensionCost" type="integer" value="0" label="extension cost" help="--extension-cost"/>
        <param name="extensionCost" type="integer" value="0" label="extension cost" help="--extension-cost"/>
        <param name="scaleAccessibility" size="8" type="float" value="1.0" label="scale all opening energy by a factor" help="--scale-accessibility"/>
        <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate structures subject to constraints. Constraints have to be given in the input file" help="--constraint"/>


        <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="fastFolding" type="select" label="Backtracking" help="--fast-folding">
                    <option value="0" selected="true">based on standard energy model (0) - normal</option>
                    <option value="2">based on approximate plex model (2) - faster</option>
                    <option value="1">no recomputation (1) - fastest</option>
                </param>
                <param name="duplexDistance" type="integer" value="0" label="Distance between target 3' ends of two consecutive duplexes" help="--duplex-distance"/>
                <param name="enThreshold" size="8" type="float" value="-100000" label="Minimum Energy Gain for a Duplex [kcal/mol]" help="--energy-threshold"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="rnaplex_input1.fa"/>
            <output name="out_file" file="rnaplex_result1.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[

**RNAplex**

Computes optimal and suboptimal secondary structures for their hybridization. The calculation is simplified by allowing only inter-molecular base pairs.


-----

**Input format**

RNALplex requires either one Fasta file or two Clustal files as input

------

**Outputs**

The computed optimal and suboptimal structure are given, 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.


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