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<tool id="rnalfold" name="RNALfold" version="2.1.6.0">
    <description>calculates locally stable secondary structures of RNA</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNALfold</token>
        <import>macros.xml</import>
    </macros>
    <command>
<![CDATA[
        RNALfold -L $span -T $temperature -d$dangling < $fasta_input | sed -r 's/(^[.()]*) +(\(.*\)) +(.*)/\1\t\2\t\3/' > $out_file
        #if $varExists('$advancedOptions.noconversion')
            #if $advancedOptions.noconversion
                --noconv
            #end if
            #if $advancedOptions.gquad
                --gquad
            #end if
            #if $advancedOptions.nolp
                --noLP
            #end if
            #if $advancedOptions.nogu
                --noGU
            #end if
            #if $advancedOptions.noclosinggu
                --noClosingGU
            #end if
            #if $advancedOptions.notetra
                --noTetra
            #end if
        #end if
]]>
    </command>
    <inputs>
	<param format="fasta" name="fasta_input" type="data" label="FASTA file"/>
        <param name="span" type="integer" min="0" max="5000" value="150" label="base pair span" help="Maximal distance between two paired bases. (-L)"/>
        <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="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>
        <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" label="no conversion" help="--noconv  do not convert thymine to uracile (T -> U)."/>
                <param name="gquad" type="boolean" checked="false" label="G Quadruplex formation" help="-g  take into account G Quadruplex formation"/>
                <param name="nolp" type="boolean" checked="false" label="No lonely pairs" help="--noLP  don't allow lonely pairs."/>
                <param name="nogu" type="boolean" checked="false" label="No GU pairing" help="--noGU  don't allow pairing of G and U."/>
                <param name="noclosinggu" type="boolean" 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" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="out_file"/>
    </outputs>
    <tests>
        <test>
            <param name="fasta_input" value="rnalfold_input1.fa"/>
            <output name="out_file" file="rnalfold_result1.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[
**RNALfold**

Compute locally stable RNA secondary structure with a maximal base pair span.
For a sequence of length n and a base pair span of L the algorithm uses only
O(n+L*L) memory and O(n*L*L) CPU time. *Thus it is practical to "scan" very
large genomes for short RNA structures*.
Output consists of a list of secondary structure components of size <= L, one
entry per line. Each output line contains the predicted local structure its
energy in kcal/mol and the starting position of the local structure.

-----

**Input format**

- RNALfold requires one input file in FASTA format

------

**Outputs**

- text output with dot-bracket notation and free energies of the secondary structures

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