<tool id="viennarna_rnaheat" name="@EXECUTABLE@" version="@VERSION@.0">
    <description>Calculate energies of RNA in a temperature range</description>
    <macros>
        <token name="@EXECUTABLE@">RNAheat</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />    
    <command>
<![CDATA[
    RNAheat < '$input' > '$output'
    --Tmin $tmin --Tmax $tmax -d$dangling --stepsize=$stepsize --ipoints=$ipoints
    #if $varExists('$advancedOptions.noconversion')
        $advancedOptions.noconversion
        $advancedOptions.nolp
        $advancedOptions.nogu
        $advancedOptions.noclosinggu
        $advancedOptions.notetra
        #if $advancedOptions.nsp
            --nsp='$advancedOptions.nsp'
        #end if
    #end if
]]>
    </command>

    <inputs>
        <param format="fasta" name="input" type="data" label="Input file"/>
        <param name="tmin" type="float" value="0.0" label="minimal temperature [°C]" help="--Tmin"/>
        <param name="tmax" type="float" value="100.0" label="maximal temperature [°C]" help="--Tmax"/>
        <param name="stepsize" type="float" value="1.0" label="stepsize [°C]" help="--stepsize"/>
        <param name="ipoints" type="integer" value="2" label="data points to fit parabola to: 2*value+1" help="--ipoints"/>
        <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>
        <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)"/>
                <param argument="--nsp" type="text" value="" label="Allow other pairs in addition to the usual AU,GC,and GU pairs."
                   help="Its argument is a comma separated list of additionally allowed pairs. If the first character is '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA  will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy." />
            </when>
            <when value="basic">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="rnaheat_input1.fa"/>
            <output name="out_file" file="rnaheat_result1.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[
**RNAheat**

Calculates the specific heat of RNA sequences in the temperature range t1 to t2, from the partition function by numeric differentiation. The program fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives. Increasing this parameter produces a smoother curve.


-----

**Input format**

RNAheat requires one input file Fasta format.


------

**Outputs**

The result is written as a list of pairs of temperature in C and specific heat in Kcal/(Mol*K) for each sequence in the input file.


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