--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnapdist.xml	Wed Oct 05 05:01:00 2016 -0400
@@ -0,0 +1,101 @@
+<tool id="veinnarna_rnadpdist" name="@EXECUTABLE@" version="@VERSION@.0">
+    <description>Calculate distances between thermodynamic RNA secondary structure ensembles
+    </description>
+
+    <macros>
+        <token name="@EXECUTABLE@">RNApdist</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+    RNApdist < '$input' > '$output'
+    --compare=$compare
+    -T$temperature -d$dangling
+    $backtrack
+    #if $varExists('$advancedOptions.nolp')
+        $advancedOptions.noconv
+        $advancedOptions.nolp
+        $advancedOptions.nogu
+        $advancedOptions.noclosinggu
+        $advancedOptions.notetra
+    #end if
+    #if $backtrack and str($compare)=="m"
+        && cat backtrack.file >> '$outfile'
+    #end if
+
+]]>
+    </command>
+
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Fasta file"/>
+        <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="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>
+        <param name="compare" type="select" label="Comparison Option" help="--compare">
+            <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="backtrack" type="boolean" checked="false" truevalue="--backtrack" falsevalue="" label="Print an alignment" help="--backtrack"/>
+        <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="noconv" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion of T -> U" help="--noconv"/>
+                <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" label="No lonely pairs" help="--noLP  don't allow lonely pairs."/>
+                <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU  don't allow pairing of G and U."/>
+                <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" label="No GU pairing at the ends" help="--noClosingGU  don't allow pairing of G and U at the ends of helices."/>
+                <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
+            </when>
+            <when value="basic">
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="output"/>
+        <data format="txt" name="dotplot"/>
+        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="rnapdist_input1.fa"/>
+            <output name="out_file" file="rnapdist_result1.txt"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+**RNApdist**
+
+RNApdist calculates structure distances between the thermodynamic ensembles of the secondary structures of RNA sequences.
+
+-----
+
+**Input format**
+
+RNApdist requires one input file
+- Fasta file
+
+------
+
+**Outputs**
+
+- output of alignment scores and alignments (if -B option is selected)
+- dot plot matrices in postscript format bundled together in a tar file
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>