' )
+
+for filename in os.listdir( sys.argv[2] ):
+ if os.path.isfile( os.path.join( sys.argv[2], filename) ) and False ==(filename.endswith('epm') or filename.endswith('fa') or filename.endswith('aln') or filename.endswith('html')):
+ o.write( ' ' % ( filename ))
+
+o.write( '' )
+o.close()
+
+# create zip file
+
+zf = zipfile.ZipFile(sys.argv[1], mode='w')
+for files in os.listdir(sys.argv[2]):
+ zf.write(files)
+zf.close()
diff -r 000000000000 -r 4699a84c41d8 exparna.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/exparna.xml Mon Dec 23 18:02:44 2013 -0500
@@ -0,0 +1,56 @@
+
+
+
+ exparna
+ EXPARNA_SCRIPT_PATH
+
+
+ExpaRNA
+-t$emp_scoring
+-s$min_incl_sub
+-n$max_used_sub
+$locarna_input
+$alignment_to_file
+$list_in_file
+$all_in_file
+$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;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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**
+ You will receive a zip file containing all output files
+
+
diff -r 000000000000 -r 4699a84c41d8 test-data/input.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fasta Mon Dec 23 18:02:44 2013 -0500
@@ -0,0 +1,4 @@
+>AF165050.379
+UUGGGGGCGACAUUCCACCAUAGAUAAUUCCCCUGUGAGGAAUUACUGUUUUAACGCAGAAAGCGUUUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCUUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGAUGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCUAAACCCCAAAGAAAAACCAAACGUAACACCAACCG
+>D45172.391
+GCCAGCCCCCUGAUGGGGGCGACACUCCACCAUAGAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCAAAACCCCAAAGAAAAAUCAAACGUAACACCAACCG
diff -r 000000000000 -r 4699a84c41d8 test-data/input.fasta~
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fasta~ Mon Dec 23 18:02:44 2013 -0500
@@ -0,0 +1,4 @@
+>AF165050.379
+UUGGGGGCGACAUUCCACCAUAGAUAAUUCCCCUGUGAGGAAUUACUGUUUUAACGCAGAAAGCGUUUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCUUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGAUGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCUAAACCCCAAAGAAAAACCAAACGUAACACCAACCG
+>D45172.391
+GCCAGCCCCCUGAUGGGGGCGACACUCCACCAUAGAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCAAAACCCCAAAGAAAAAUCAAACGUAACACCAACCG
diff -r 000000000000 -r 4699a84c41d8 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Dec 23 18:02:44 2013 -0500
@@ -0,0 +1,24 @@
+
+
+
+
+
+
+
+
+ http://www.bioinf.uni-freiburg.de/Software/expaRNA/exparna-1.0.tar.gz
+
+
+
+
+
+ ./configure --prefix $INSTALL_DIR --with-RNA=$ROOT_VIENNA_RNA_DIR
+
+
+ $INSTALL_DIR/bin
+
+
+
+ Compiling ExpaRNA requires a C compiler (typically gcc)
+
+