--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnalalifold.xml	Wed Oct 05 05:00:07 2016 -0400
@@ -0,0 +1,97 @@
+<tool id="veinnarna_rnalalifold" name="@EXECUTABLE@" version="@VERSION@.0">
+    <description>Calculate locally stable secondary structures for a set of aligned RNAs</description>
+    <macros>
+        <token name="@EXECUTABLE@">RNALalifold</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+    RNALalifold '$input' > '$output'
+    -T$temperature -d$dangling
+    -L$span
+    $mis
+    #if $varExists('$advancedOptions.nolp')
+        $advancedOptions.nolp
+        $advancedOptions.nogu
+        $advancedOptions.noclosinggu
+        $advancedOptions.notetra
+        --cfactor=$advancedOptions.cfactor
+        --nfactor=$advancedOptions.nfactor
+        $advancedOptions.ribosum
+    #end if
+]]>
+    </command>
+
+    <inputs>
+        <param format="txt" name="input" type="data" label="Clustal file"/>
+        <param name="span" type="integer" min="0" max="5000" value="60" 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="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>
+        <!-- the -p option led to segmentation faults with version 2.1.2 and 2.1.7, it was later removed from verion 2.1.10 -->
+        <!--<param name="pf" type="boolean" checked="false" truevalue="-p" falsevalue="" label="calculate partition function" help="-p"/>-->
+        <param name="mis" type="boolean" checked="false" truevalue="--mis" falsevalue="" label="Most Informative Sequence" help="--mis"/>
+        <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">
+               <!-- the -cutoff option was removed from version 2.2.10 -->
+                <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"/>
+                <param name="cfactor" type="float" value="1.0" label="Weight of the covariance term" help="--cfactor"/>
+                <param name="nfactor" type="float" value="1.0" label="Penalty for non-compatible sequences in the covariance term" help="--nfactor"/>
+                <param name="ribosum" type="boolean" truevalue="--ribosum_scoring" falsevalue="" checked="false" label="Use ribosum scoring matrix" help="--ribosum_scoring"/>
+            </when>
+            <when value="basic">
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="output" />
+        <!-- the program does not seem to generate a dot plot, even though that is implied in the help -->
+        <!--<data format="tar" name="imagesFile" label="RNALalifold images"/>-->
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="rnalalifold_input1.clustal"/>
+            <output name="output" file="rnalalifold_result1.txt"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+**RNALalifold**
+
+Calculates 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
+
+
+-----
+
+**Input format**
+
+RNALalifold requires one input file
+- Clustal file
+
+------
+
+**Outputs**
+
+- energy of the consensus structures in the clustal file
+- several possible postscript images bundled together in a tar file
+
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>