<tool id="viennarna_rnapaln" name="@EXECUTABLE@" version="@VERSION@.0">
    <description>RNA alignment based on sequence base pairing propensities
    </description>
    <macros>
        <token name="@EXECUTABLE@">RNApaln</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
    RNApaln < '$input' > '$output'
    --mode=$alignmentmode
    -T$temperature -d$dangling
    $backtrack
    --gapo=$gapo
    --gape=$gape
    --seqw=$seqw
    $endgaps
    #if $varExists('$advancedOptions.nolp')
        $advancedOptions.noconversion
        $advancedOptions.nolp
        $advancedOptions.nogu
        $advancedOptions.noclosinggu
        $advancedOptions.notetra
    #end if
    #if $backtrack and str($alignmentmode)=="m"
        && cat backtrack.file >> '$outfile'
    #end if
]]>
    </command>

    <inputs>
        <param format="fasta" name="input" type="data" label="Fasta file"/>
        <param name="temperature" 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="alignmentmode" type="select" label="Comparison Option" help="--mode">
            <option value="p" selected="True">p: pairwise (1st with 2nd, 3rd with 4th, ...)</option>
            <option value="m">m: matrix (each with each, output in matrix form)</option>
            <option value="f" >f: first (1st with 2nd, 1st with 3rd, ...)</option>
            <option value="c">c: continuous (1st with 2nd, 2nd with 3rd, ...)</option>
        </param>

        <!-- In versions 2.1.2, 2.1.7, and 2.2.10 the alignment score is wrong if -B is not selected, therefore the default for this option is set to true -->
        <param name="backtrack" type="boolean" checked="true" truevalue="-B" falsevalue="" label="Print an alignment" help="-B"/>

        <param name="gapo" type="float" value="1.5" label="gap open penalty" help="--gapo"/>
        <param name="gape" type="float" value="0.67" label="gap extension penalty" help="--gape"/>
        <param name="seqw" type="float" value="0.5" label="weight of sequence compared to structure" help="--seqw"/>
        <param name="endgaps" type="boolean" checked="false" truevalue="--endgaps" falsevalue="" label="Allow free end-gaps" help="--endgaps"/>

        <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="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
                <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
                <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/>
                <param name="notetra" type="boolean" truevalue="" falsevalue="--noTetra" checked="true" label="Allow stabilization for loops, hairpins etc." help=" Include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (--noTetra)"/>
                <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>                
            </when>
            <when value="basic">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="output"/>
        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="rnapaln_input1.fa"/>
            <output name="out_file" file="rnapaln_result1.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[

**RNApaln**

RNA alignment based on sequence base pairing propensities.

Uses string-alignment techniques to perform fast pairwise structural alignments of RNAs. Similar to RNApdist secondary structure is incorporated in an approximate manner by computing base pair probabilities, which are then reduced to a vector holding the probability that a base is paired upstream, downstream, or remains unpaired. Such pair propsensity vectors can then be compared using standard alignment algorithms. In contrast to RNApdist, RNApaln performs similarity (instead of distance) alignments, considers both sequence and structure information, and uses affine (rather than linear) gap costs. RNApaln can perform semi-local alignments by using free end gaps, a true local alignment mode is planned.

-----

**Input format**

RNApaln requires one input file
- Fasta file

------

**Outputs**

- output of alignment scores and alignments (if -B option is selected)
- dot plot matrices in postscript format bundled together in a tar file

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