--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaeval.xml	Tue Feb 03 04:59:51 2015 -0500
@@ -0,0 +1,77 @@
+<tool id="rnaeval" name="RNAeval" version="2.1.6.0">
+    <description>Calculate energy of RNA sequences with given secondary structure</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@EXECUTABLE@">RNAeval</token>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+<![CDATA[
+        RNAeval < $input > $tabularFile
+        -T$temperature -d$dangling
+        #if $varExists('$advancedOptions.noconversion')
+            $advancedOptions.noconversion
+            $advancedOptions.verbose
+            $advancedOptions.gquad
+            $advancedOptions.circ
+            $advancedOptions.logml
+            $advancedOptions.notetra
+        #end if
+]]>
+    </command>
+
+    <inputs>
+        <param format="text" name="input" type="data" label="Input file"/>
+        <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="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="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No converstion from T->U" help="--noconv"/>
+                <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Print out energy of each loop in the structure." help="--verbose"/>
+                <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G-quadruplex formation prediction" help="--gquad"/>
+                <param name="circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA" help="--circ"/>
+                <param name="logml" type="boolean" truevalue="--logML" falsevalue="" checked="false" label="Logarithmic energy functions for multi-loops" help="--logML"/>
+                <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="tabularFile"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+**RNAeval**
+RNAeval evaluates the free energy of an RNA molecule in fixed secondary structure. Sequences and structures are read alternately from stdin. The energy in Kcal/Mol is written to stdout.
+
+-----
+
+**Input format**
+
+RNAeval requires one input file in a format similar to the Fasta format. The secondary strucures should be added after the sequence in dot-bracket notation. Sequence and structure can be interupted by an '&' to calculate the co-folding of two RNA-strands.
+
+
+------
+
+**Outputs**
+
+First line: the sequence, second line: the structure with its corresponding energy
+
+
+]]>
+    </help>
+    <expand macro="requirements" />
+</tool>