--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaheat.xml	Tue Dec 06 12:31:31 2016 -0500
@@ -0,0 +1,90 @@
+<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>