--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnadistance.xml	Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,82 @@
+<tool id="rnadistance" name="RNAdistance" version="2.1.6.0">
+    <description>Calculate distance between secondary structures of two RNAs</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@EXECUTABLE@">RNAdistance</token>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+<![CDATA[
+        RNAdistance < $input > $outfile
+        --distance=#echo ''.join(str($distance).split(','))#
+        --compare=$compare
+        $shapiro
+        $backtrack
+        #if $backtrack and str($compare)=="m"
+            ; cat backtrack.file >> $outfile
+        #end if
+]]>
+    </command>
+
+    <inputs>
+        <param name="input" type="data" label="Primary and secondary stuctures file"/>
+        <param name="distance" type="select" multiple="true" display="checkboxes" label="Representation to calculate the distance / alignment option">
+                <option value="f" selected="true">full/tree</option>
+                <option value="F">full/string</option>
+                <option value="h">hit/tree</option>
+                <option value="H">hit/string</option>
+                <option value="w">weighted coarse/tree</option>
+                <option value="W">weighted coarse/string</option>
+                <option value="c">coarse/tree</option>
+                <option value="C">coarse/string</option>
+                <validator type="no_options" message="Please select at least one type."/>
+        </param>
+        <param name="compare" type="select" label="Comparison Option" help="-d">
+            <option value="p" selected="True">p: pairwise (1st with 2nd, 3rd with 4th, ...)</option>
+            <option value="m">m: matrix (each with each, output in matrix form)</option>
+            <option value="f" >f: first (1st with 2nd, 1st with 3rd, ...)</option>
+            <option value="c">c: continuous (1st with 2nd, 2nd with 3rd, ...)</option>
+        </param>
+        <param name="shapiro" type="boolean" checked="false" truevalue="--shapiro" falsevalue="" label="Use cost matrix by Bruce Shapiro" help="--shapiro"/>
+        <param name="backtrack" type="boolean" checked="false" truevalue="--backtrack" falsevalue="" label="Print an alignment" help="--backtrack"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="outfile"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+**RNAdistance**
+
+
+-----
+
+**Input format**
+
+RNAdistance requires one input file with the following structure:
+1st line: can be a comment line like in Fasta, begins with '>'
+2nd line: sequence
+3rd line: first secondary structure in dot-bracket notation
+4th line: second secondary structure in dot-bracket notation
+...
+nth line: another sequence
+...
+
+Several different RNA secondary structures can be specified. The input has a Fasta-like structure but with secondary structure information.
+
+
+------
+
+**Outputs**
+
+* distance of the structures
+* with the backtrack options it is possible to get alignment ouput
+
+
+]]>
+    </help>
+    <expand macro="requirements" />
+</tool>