--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnalfold.xml	Tue Dec 06 12:31:55 2016 -0500
@@ -0,0 +1,97 @@
+<tool id="viennarna_rnalfold" name="@EXECUTABLE@" version="@VERSION@.0">
+    <description>calculates locally stable secondary structures of RNA</description>
+
+    <macros>
+        <token name="@EXECUTABLE@">RNALfold</token>
+        <import>macros.xml</import>
+    </macros>
+        <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+    RNALfold -L $span -T $temperature -d$dangling < '$fasta_input' 
+    #if $varExists('$advancedOptions.noconversion')
+        $advancedOptions.noconversion
+        $advancedOptions.gquad
+        $advancedOptions.nolp
+        $advancedOptions.nogu
+        $advancedOptions.noclosinggu
+        $advancedOptions.notetra
+        #if $advancedOptions.activateZscore 
+            #if str($advancedOptions.zscore) <> ""
+                --zscore=$advancedOptions.zscore
+            #else
+                --zscore
+            #end if
+        #end if
+    #end if
+    | sed -r 's/(^[.()]*) +(\(.*\)) +(.*)/\1\t\2\t\3/' > '$out_file'
+]]>
+    </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" 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="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="Take G Quadruplex formation into account" argument="-g"/>
+                <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 name="activateZscore" type="boolean" checked="false" label="Activate Z−score computation. An optional argument may be supplied to set the threshold" help="(--zscore)"/>
+                <param name="zscore" type="float" value="-2" optional="true" label="Z-score" help="An optional argument may be supplied to set the threshold"/>
+            </when>
+            <when value="basic">
+            </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="citations" />
+</tool>