<tool id="rnadistance" name="RNAdistance" version="2.1.6.0">
    <description>Calculate distance between secondary structures of two RNAs</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNAdistance</token>
        <import>macros.xml</import>
    </macros>
    <command>
<![CDATA[
        RNAdistance < $input > $outfile
        --distance=#echo ''.join(str($distance).split(','))#
        --compare=$compare
        $shapiro
        $backtrack
        #if $backtrack and str($compare)=="m"
            ; cat backtrack.file >> $outfile
        #end if
]]>
    </command>

    <inputs>
        <param name="input" type="data" label="Primary and secondary stuctures file"/>
        <param name="distance" type="select" multiple="true" display="checkboxes" label="Representation to calculate the distance / alignment option">
                <option value="f" selected="true">full/tree</option>
                <option value="F">full/string</option>
                <option value="h">hit/tree</option>
                <option value="H">hit/string</option>
                <option value="w">weighted coarse/tree</option>
                <option value="W">weighted coarse/string</option>
                <option value="c">coarse/tree</option>
                <option value="C">coarse/string</option>
                <validator type="no_options" message="Please select at least one type."/>
        </param>
        <param name="compare" type="select" label="Comparison Option" help="-d">
            <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>
        <param name="shapiro" type="boolean" checked="false" truevalue="--shapiro" falsevalue="" label="Use cost matrix by Bruce Shapiro" help="--shapiro"/>
        <param name="backtrack" type="boolean" checked="false" truevalue="--backtrack" falsevalue="" label="Print an alignment" help="--backtrack"/>
    </inputs>
    <outputs>
        <data format="txt" name="outfile"/>
    </outputs>
    <tests>
    </tests>
    <help>
<![CDATA[
**RNAdistance**


-----

**Input format**

RNAdistance requires one input file with the following structure:
1st line: can be a comment line like in Fasta, begins with '>'
2nd line: sequence
3rd line: first secondary structure in dot-bracket notation
4th line: second secondary structure in dot-bracket notation
...
nth line: another sequence
...

Several different RNA secondary structures can be specified. The input has a Fasta-like structure but with secondary structure information.


------

**Outputs**

* distance of the structures
* with the backtrack options it is possible to get alignment ouput


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