# HG changeset patch
# User bernhardlutz
# Date 1388261350 18000
# Node ID 51e200ccf18eafac04b3124c670862cd0c747284
# Parent  4699a84c41d81211f3f69c063b0057f01c96a81c
Uploaded

diff -r 4699a84c41d8 -r 51e200ccf18e exparna.xml
--- a/exparna.xml	Mon Dec 23 18:02:44 2013 -0500
+++ b/exparna.xml	Sat Dec 28 15:09:10 2013 -0500
@@ -7,8 +7,10 @@
     <command>
 ExpaRNA 
 -t$emp_scoring
+#if $check == "no":
+-n$max_used_sub
+#end if
 -s$min_incl_sub
--n$max_used_sub
 $locarna_input
 $alignment_to_file
 $list_in_file
@@ -16,7 +18,7 @@
 $fastafile;
     mkdir $outfile.files_path;
     cp ./ExpaRNA-results/* $outfile.files_path;
-    python /home/bernhard/galaxytools/rna_tools/exparna/create_html.py $outfile $outfile.files_path;
+    python \$EXPARNA_SCRIPT_PATH/create_html.py $outfile $outfile.files_path;
     </command>
     <stdio>
         <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
@@ -48,7 +50,8 @@
     </outputs>
     <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.
+    
+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**
     You will receive a zip file containing all output files 
diff -r 4699a84c41d8 -r 51e200ccf18e tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Dec 23 18:02:44 2013 -0500
+++ b/tool_dependencies.xml	Sat Dec 28 15:09:10 2013 -0500
@@ -13,10 +13,17 @@
                     </repository>
                 </action>
                 <action type="shell_command">./configure --prefix $INSTALL_DIR --with-RNA=$ROOT_VIENNA_RNA_DIR</action>
-                 <action type="make_install" />
+                <action type="make_install" />
+                <action type="move_file">
+                    <source>create_html.py</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                 </action>
+                <action type="set_environment">
+                    <environment_variable action="set" name="EXPARNA_SCRIPT_PATH">$INSTALL_DIR</environment_variable>
+                </action>
             </actions>
         </install>
         <readme>Compiling ExpaRNA requires a C compiler (typically gcc)</readme>