# HG changeset patch
# User bernhardlutz
# Date 1389294679 18000
# Node ID 683f4c13662dc013df52fa1e6f8d48ba10086b8b
# Parent  b75c2fe4cf88ce0d56df09816a8b4df0e281b648
Uploaded

diff -r b75c2fe4cf88 -r 683f4c13662d exparna.xml
--- a/exparna.xml	Thu Jan 09 12:54:13 2014 -0500
+++ b/exparna.xml	Thu Jan 09 14:11:19 2014 -0500
@@ -19,6 +19,9 @@
     mkdir $outfile.files_path;
     cp ./ExpaRNA-results/* $outfile.files_path;
     python \$EXPARNA_SCRIPT_PATH/create_html.py $outfile $outfile.files_path;
+#if $locarna_input:
+    cp ./ExpaRNA-results/LCSEPM_LocARNA_* $locarna_inputfile
+#end if
     </command>
     <stdio>
         <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
@@ -46,14 +49,27 @@
         <param name="all_in_file" type="boolean" checked="false" truevalue="-a" falsevalue="" label="Write all EPMs into file" help="-a" />
     </inputs>
     <outputs>
+    <data format="fasta" name="locarna_inputfile" label="Output generated for Locarna">
+          <filter>locarna_input is True</filter>
+        </data>
         <data name="outfile" format="zip" />
     </outputs>
+    <tests>
+      <test>
+          <param name="fastafile" value="input.fasta" />
+          <output name="output" file="output.zip" compare="sim_size" />
+          <param name="locarna_input" value=""  />
+          <param name="check_all" value="yes"  />
+      </test>
+
+    </tests>
     <help>**What it does**
     http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp
     
 ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Instead of computing a full sequence-structure alignment, it computes the best arrangement of sequence-structure motifs common to two RNAs. A motif is a local (or isolated) substructure which is identical to both RNAs. ExpaRNA requires a given nested secondary structure for both RNAs. If no structure is available, RNAfold from Vienna RNA Package is used for a structure prediction. The accuracy of the algorithm is mainly controlled by the minimal size of the included sequence-structure motifs. ExpaRNA is especially useful for comparative structural RNA analysis and to speed-up complex sequence-structure alignment methods. For this purpose, the predicted common substructures by ExpaRNA are used as anchor constraints for a full structural alignment.
+
+**Output**
     
-    **Output**
-    You will receive a zip file containing all output files 
+You will receive a zip file containing all output files and optionally the outputfile made for postprocessing with locarna.
     </help>
 </tool>