# HG changeset patch
# User rnateam
# Date 1423506371 18000
# Node ID 5e58cbf27a05c350ec0e26262c2ff0c749c256ea
# Parent  ec0fdb8c4ebbf748dbf83c3f48acdbf1d5269a61
Uploaded

diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rna2dfold.xml
--- a/rna2dfold.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rna2dfold.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -78,6 +78,11 @@
         <data format="txt" name="out_file"/>
     </outputs>
     <tests>
+        <test>
+            <param name="custom_input" value="rna2dfold_input1.txt"/>
+            <param name="nrbt" value="0"/>
+            <output name="out_file1" file="rna2dfold_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaaliduplex.xml
--- a/rnaaliduplex.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnaaliduplex.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -51,6 +51,11 @@
         <data format="txt" name="out_file"/>
     </outputs>
     <tests>
+        <test>
+            <param name="input1" value="rnaaliduplex_input1.clustal"/>
+            <param name="input2" value="rnaaliduplex_input1.clustal"/>
+            <output name="out_file1" file="rnaaliduplex_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaalifold.xml
--- a/rnaalifold.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnaalifold.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -93,6 +93,10 @@
         <data format="tar" name="imagesFile"/>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="rnaalifold_input1.clustal"/>
+            <output name="output" file="rnaalifold_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnacofold.xml
--- a/rnacofold.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnacofold.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -62,6 +62,10 @@
         </collection>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="rnacofold_input1.fas"/>
+            <output name="out_file" file="rnacofold_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnadistance.xml
--- a/rnadistance.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnadistance.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -46,6 +46,10 @@
         <data format="txt" name="outfile"/>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="rnadistance_input1.fas"/>
+            <output name="outfile" file="rnadistance_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaduplex.xml
--- a/rnaduplex.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnaduplex.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -51,6 +51,10 @@
         <data format="txt" name="tabularFile"/>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="rnaduplex_input1.fa"/>
+            <output name="out_file" file="rnaduplex_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaeval.xml
--- a/rnaeval.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnaeval.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -51,6 +51,10 @@
         <data format="txt" name="tabularFile"/>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="rnaeval_input1.fas"/>
+            <output name="out_file" file="rnaeval_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnafold.xml
--- a/rnafold.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnafold.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -78,6 +78,15 @@
           
     </outputs>
     <tests>
+        <test>
+            <param name="fasta_input" value="rnafold_input1.fa"/>
+            <output name="out_file1" file="rnafold_result1.txt"/>
+        </test>
+        <test>
+            <param name="fasta_input" value="rnafold_input2.fa"/>
+            <param name="temperature" value="75"/>
+            <output name="out_file1" file="rnafold_result2.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaheat.xml
--- a/rnaheat.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnaheat.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -52,6 +52,10 @@
         <data format="txt" name="output"/>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="rnaheat_input1.fa"/>
+            <output name="out_file" file="rnaheat_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnainverse.xml
--- a/rnainverse.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnainverse.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -57,6 +57,14 @@
         <data format="txt" name="outfile"/>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="rnainverse_input1.fas"/>
+            <output name="outfile">
+                <assert_contents>
+                    <has_line_matching expression="^gggccccnnaauun.*"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnalalifold.xml
--- a/rnalalifold.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnalalifold.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -24,7 +24,6 @@
             --nfactor=$advancedOptions.nfactor
             $advancedOptions.ribosum
         #end if
-        <!--; tar -cf $imagesFile *.ps -->
 ]]>
     </command>
 
@@ -68,6 +67,10 @@
         <!--<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[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnalfold.xml
--- a/rnalfold.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnalfold.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -61,6 +61,10 @@
         <data format="txt" name="out_file"/>
     </outputs>
     <tests>
+        <test>
+            <param name="fasta_input" value="rnalfold_input1.fa"/>
+            <output name="out_file" file="rnalfold_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnapaln.xml
--- a/rnapaln.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnapaln.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -78,6 +78,10 @@
         </collection>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="rnapaln_input1.fa"/>
+            <output name="out_file" file="rnapaln_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnapdist.xml
--- a/rnapdist.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnapdist.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -62,12 +62,16 @@
     </inputs>
     <outputs>
         <data format="txt" name="output"/>
-        <data format="txt" name="dotplot">
+        <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[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnapkplex.xml
--- a/rnapkplex.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnapkplex.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -54,6 +54,10 @@
         </collection>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="rnapkplex_input1.fa"/>
+            <output name="out_file" file="rnapkplex_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaplex.xml
--- a/rnaplex.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnaplex.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -98,6 +98,10 @@
         <data format="txt" name="output"/>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="rnaplex_input1.fa"/>
+            <output name="out_file" file="rnaplex_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaplfold.xml
--- a/rnaplfold.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnaplfold.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -78,6 +78,10 @@
         <data format="tar" name="outputf"/>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="rnaplfold_input1.fa"/>
+            <output name="out_file" file="rnaplfold_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaplot.xml
--- a/rnaplot.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnaplot.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -49,6 +49,14 @@
         <data format="tar" name="imagesFile"/>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="rnaplot_input1.fas"/>
+            <output name="imagesFile">
+                <assert_contents>
+                    <has_line line="%%Title: RNA Secondary Structure Plot"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnasnoop.xml
--- a/rnasnoop.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnasnoop.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -10,7 +10,7 @@
     <command>
 <![CDATA[
         RNAsnoop --query=$input1 --target=$input2 > $output
-        --alignmentLenght=$length
+        --alignmentLength=$length
         $constraint
         --energy-threshold=$energyThreshold
         #if $varExists('$advancedOptions.extensioncost')
@@ -99,6 +99,11 @@
 
     </outputs>
     <tests>
+        <test>
+            <param name="input1" value="rnasnoop_input1b.fa"/>
+            <param name="input2" value="rnasnoop_input1a.fa"/>
+            <output name="output" file="rnasnoop_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnasubopt.xml
--- a/rnasubopt.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnasubopt.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -93,6 +93,10 @@
         <data format="txt" name="output"/>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="rnasubopt_input1.fa"/>
+            <output name="output" file="rnasubopt_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaup.xml
--- a/rnaup.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/rnaup.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -80,6 +80,10 @@
         <data format="tar" name="accesibilitiesFile"/>
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="rnaup_input1.fa"/>
+            <output name="output" file="rnaup_result1.txt"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rna2dfold_input1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rna2dfold_input1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))..
+.((((((..(((..........))).(((((.......))))).....(((((.......)))))))))))..
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rna2dfold_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rna2dfold_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,6 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-21.90)
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-21.90) <ref 1>
+.((((((..(((..........))).(((((.......))))).....(((((.......))))))))))).. (-17.20) <ref 2>
+k	l	en	structure
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaaliduplex_input1.clustal
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaaliduplex_input1.clustal	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,7 @@
+CLUSTAL 2.1 multiple sequence alignment
+
+
+Anolis_carolinensis_chrUn_GL34      TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+Anolis_carolinensis_chrUn_GL35      GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
+                                     ************************************** ************** ******* ********* 
+
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaaliduplex_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaaliduplex_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,1 @@
+(((((((..(.......((((..(..((((((..((((((.......((((((..(..(((((..(((((((.&)))))))..).......))))..)..))))))..)))))).......))))))..)..)))))..))))))).   1,73  :   1,73  (-39.70)
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaalifold_input1.clustal
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaalifold_input1.clustal	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,7 @@
+CLUSTAL 2.1 multiple sequence alignment
+
+
+Anolis_carolinensis_chrUn_GL34      TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+Anolis_carolinensis_chrUn_GL35      GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
+                                     ************************************** ************** ******* ********* 
+
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaalifold_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaalifold_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,2 @@
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUCGAUGCCCACAUUCUCCA
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-25.85 = -25.60 +  -0.25) 
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnacofold_input1.fas
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnacofold_input1.fas	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,2 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA&UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnacofold_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnacofold_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,3 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA&UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((((((((.(((((((((((..&.))))))..((((........)))).(((((.......))))).....))))))))))).))))))))))).. (-55.70)
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnadistance_input1.fas
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnadistance_input1.fas	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,2 @@
+.((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))..
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))).
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnadistance_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnadistance_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,1 @@
+f: 4  
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaduplex_input1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaduplex_input1.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaduplex_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaduplex_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,3 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC
+.((((((..((......((((...((((..(((.((((((.......((((((..(..((((...(((((((.&)))))))..........))))..)..))))))..))))))..)))..)))).......)))).)))))))).   1,73  :   1,72  (-40.30)
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaeval_input1.fas
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaeval_input1.fas	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,3 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))..
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaeval_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaeval_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,2 @@
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-21.90)
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnafold_input1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnafold_input1.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnafold_input2.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnafold_input2.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnafold_output1.tar
Binary file test-data/rnafold_output1.tar has changed
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnafold_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnafold_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,6 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-21.90)
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-28.70)
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnafold_result2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnafold_result2.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,6 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+......................(((....)))........(((((...(((((.......))))).))))).. ( -3.39)
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
+(((((((...............(((....)))................(((((.......)))))))))))). ( -4.71)
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaheat_input1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaheat_input1.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,2 @@
+> comment 1
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaheat_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaheat_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,102 @@
+> comment 1
+0   0.0504916
+1   45.2129
+2   -22.6074
+3   -45.4315
+4   -22.7654
+5   45.8852
+6   0.0698557
+7   0.0752356
+8   0.0811424
+9   0.0878275
+10   0.0952985
+11   0.103563
+12   0.11263
+13   0.122506
+14   0.134201
+15   0.147482
+16   0.161608
+17   0.177852
+18   0.196997
+19   0.216779
+20   0.238736
+21   0.264173
+22   0.292607
+23   0.322778
+24   0.357032
+25   0.395149
+26   0.437165
+27   0.482593
+28   0.532254
+29   0.586448
+30   0.645484
+31   0.708343
+32   0.775859
+33   0.84754
+34   0.922752
+35   1.00153
+36   1.08295
+37   1.16636
+38   1.25124
+39   1.3361
+40   1.42079
+41   1.5038
+42   1.58485
+43   1.66306
+44   1.73829
+45   1.80923
+46   1.87712
+47   1.94176
+48   2.00355
+49   2.06245
+50   2.11985
+51   2.1763
+52   2.23277
+53   2.28969
+54   2.34834
+55   2.40888
+56   2.47175
+57   2.53748
+58   2.60638
+59   2.67862
+60   2.75422
+61   2.83314
+62   2.91548
+63   3.00222
+64   3.09214
+65   3.1846
+66   3.28007
+67   3.38221
+68   3.4979
+69   3.61577
+70   3.73136
+71   3.85079
+72   3.98807
+73   4.13409
+74   4.28792
+75   4.45835
+76   4.63996
+77   4.83693
+78   5.05746
+79   5.29359
+80   5.51312
+81   5.69891
+82   5.84747
+83   5.9541
+84   6.02318
+85   6.0546
+86   6.04743
+87   5.99966
+88   5.92173
+89   5.8316
+90   5.7362
+91   5.63003
+92   5.50616
+93   5.36588
+94   5.21371
+95   5.0571
+96   4.90551
+97   4.77223
+98   4.66389
+99   4.57469
+100   4.49084
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnainverse_input1.fas
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnainverse_input1.fas	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,2 @@
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))).
+gggccccnnaauunnnnnnnnaauunGGGGcnnnnnnnAAAAAnnnnnuuuuannnnnnnuaaaaggggcccn
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnalalifold_input1.clustal
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnalalifold_input1.clustal	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,7 @@
+CLUSTAL 2.1 multiple sequence alignment
+
+
+Anolis_carolinensis_chrUn_GL34      TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+Anolis_carolinensis_chrUn_GL35      GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
+                                     ************************************** ************** ******* ********* 
+
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnalalifold_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnalalifold_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+(((.(((((.(((((.......))))).)...(((((.......))))).))))))) (-18.55)   17 -   73
+((((........)))). ( -5.10)   10 -   26
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUCGAUGCCCACAUUCUCCA
+
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnalfold_input1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnalfold_input1.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnalfold_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnalfold_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,31 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+.((((....)))).	( -0.20)	56
+.(((..((((....)))).))).	( -3.60)	51
+.(((((.......))))).	( -7.30)	48
+.((((..(((((.......)))))..)))).	(-10.80)	42
+.(((((...(((((.......))))).))))).	(-11.70)	40
+.((.(((((...(((((.......))))).)))))))	(-12.10)	37
+.((((.......)))).	( -2.60)	27
+.(.(((((.......))))).).	( -6.20)	24
+.((((....)))).	( -2.50)	21
+.((.((((....)))).)).	( -4.90)	18
+.(((.(((.(.((((....))))).))).))).	( -7.30)	11
+.((((........)))).	( -5.20)	9
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).	(-21.90)	1
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+ (-21.90)
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+.((((....)))).	( -0.30)	56
+.(((..((((....)))).))).	( -3.60)	51
+.(((((.......))))).	( -8.80)	48
+.((((..(((((.......)))))..)))).	(-12.30)	42
+.(((((...(((((.......))))).))))).	(-12.90)	40
+.((.(((((...(((((.......))))).)))))))	(-13.60)	37
+.((((.......)))).	( -4.50)	27
+.(.(((((.......))))).).	( -8.10)	24
+.((((.(((((.......))))).)...(((((.......)))))...))).	(-17.70)	21
+.(((.(((((.(((((.......))))).)...(((((.......))))).)))))))	(-19.50)	16
+.((((........)))).	( -5.20)	9
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))).	(-28.70)	1
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
+ (-28.70)
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnapaln_input1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnapaln_input1.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnapaln_input1.fas
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnapaln_input1.fas	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,1 @@
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA&UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnapaln_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnapaln_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,7 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+68.8704
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+,((((((..((((........)))).(((((.......))))).....(((((.......)))))))))})},
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))).
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnapdist_input1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnapdist_input1.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnapdist_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnapdist_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,3 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+8.71852
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnapkplex_input1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnapkplex_input1.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnapkplex_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnapkplex_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,6 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).[[[.(((((]]]....))))))))))).. (-31.38)
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
+(((((((..((((..[[[.[[)))).(((((.]].]]]))))).....(((((.......)))))))))))). (-37.04)
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaplex_input1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaplex_input1.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaplex_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaplex_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+.((((((.......((((((..(..((((...(((((((.&)))))))..........))))..)..))))))..))))))  34,73  :   1,40  (-24.40)
+
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaplfold_input1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaplfold_input1.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaplfold_result1.txt
Binary file test-data/rnaplfold_result1.txt has changed
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaplot_input1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaplot_input1.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaplot_input1.fas
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaplot_input1.fas	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,3 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-21.90)
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnasnoop_input1a.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnasnoop_input1a.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,2 @@
+>homo
+CGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAAAAGAAACUAACCAGGAUUCCCUCAGUAACGGCGAGUGAACAGGGAAGAGCCCAGCGCCGAAUCCCCGCCCCGCGGGGCGCGGGACAUGUGGCGUACGGAAGACCCGCUCCCCGGCGCCGCUCGUGGGGGGCCCAAGUCCUUCUGAUCGAGGCCCAGCCCGUGGACGGUGUGAGGCCGGUAGCGGCCGGCGCGCGCCCGGGUCUUCCCGGAGUCGGGUUGCUUGGGAAUGCAGCCCAAAGCGGGUGGUAAACUCCAUCUAAGGCUAAAUACCGGCACGAGACCGAUAGUCAACAAGUACCGUAAGGGAAAGUUGAAAAGAACUUUGAAGAGAGAGUUCAAGAGGGCGUGAAACCGUUAAGAGGUAAACGGGUGGGGUCCGCGCAGUCCGCCCGGAGGAUUCAACCCGGCGGCGGGUCCGGCCGUGUCGGCGGCCCGGCGGAUCUUUCCCGCCCCCCGUUCCUCCCGACCCCUCCACCCGCCCUCCCUUCCCCCGCCGCCCCUCCUCCUCCUCCCCGGAGGGGGCGGGCUCCGGCGGGUGCGGGGGUGGGCGGGCGGGGCCGGGGGUGGGGUCGGCGGGGGACCGUCCCCCGACCGGCGACCGGCCGCCGCCGGGCGCAUUUCCACCGCGGCGGUGCGCCGCGACCGGCUCCGGGACGGCUGGGAAGGCCCGGCGGGGAAGGUGGCUCGGGGGGCCCCGUCCGUCCGUCCGUCCUCCUCCUCCCCCGUCUCCGCCCCCCGGCCCCGCGUCCUCCCUCGGGAGGGCGCGCGGGUCGGGGCGGCGGCGGCGGCGGCGGUGGCGGCGGCGGCGGGGGCGGCGGGACCGAAACCCCCCCCGAGUGUUACAGCCCCCCCGGCAGCAGCACUCGCCGAAUCCCGGGGCCGAGGGAGCGAGACCCGUCGCCGCGCUCUCCCCCCUCCCGGCGCCCACCCCCGCGGGGAAUCCCCCGCGAGGGGGGUCUCCCCCGCGGGGGCGCGCCGGCGUCUCCUCGUGGGGGGGCCGGGCCACCCCUCCCACGGCGCGACCGCUCUCCCACCCCUCCUCCCCGCGCCCCCGCCCCGGCGACGGGGGGGGUGCCGCGCGCGGGUCGGGGGGCGGGGCGGACUGUCCCCAGUGCGCCCCGGGCGGGUCGCGCCGUCGGGCCCGGGGGAGGUUCUCUCGGGGCCACGCGCGCGUCCCCCGAAGAGGGGGACGGCGGAGCGAGCGCACGGGGUCGGCGGCGACGUCGGCUACCCACCCGACCCGUCUUGAAACACGGACCAAGGAGUCUAACACGUGCGCGAGUCGGGGGCUCGCACGAAAGCCGCCGUGGCGCAAUGAAGGUGAAGGCCGGCGCGCUCGCCGGCCGAGGUGGGAUCCCGAGGCCUCUCCAGUCCGCCGAGGGCGCACCACCGGCCCGUCUCGCCCGCCGCGCCGGGGAGGUGGAGCACGAGCGCACGUGUUAGGACCCGAAAGAUGGUGAACUAUGCCUGGGCAGGGCGAAGCCAGAGGAAACUCUGGUGGAGGUCCGUAGCGGUCCUGACGUGCAAAUCGGUCGUCCGACCUGGGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCCUCCGAAGUUUCCCUCAGGAUAGCUGGCGCUCUCGCAGACCCGACGCACCCCCGCCACGCAGUUUUAUCCGGUAAAGCGAAUGAUUAGAGGUCUUGGGGCCGAAACGAUCUCAACCUAUUCUCAAACUUUAAAUGGGUAAGAAGCCCGGCUCGCUGGCGUGGAGCCGGGCGUGGAAUGCGAGUGCCUAGUGGGCCACUUUUGGUAAGCAGAACUGGCGCUGCGGGAUGAACCGAACGCCGGGUUAAGGCGCCCGAUGCCGACGCUCAUCAGACCCCAGAAAAGGUGUUGGUUGAUAUAGACAGCAGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUAGCCCUGAAAAUGGAUGGCGCUGGAGCGUCGGGCCCAUACCCGGCCGUCGCCGGCAGUCGAGAGUGGACGGGAGCGGCGGGGGCGGCGCGCGCGCGCGCGCGUGUGGUGUGCGUCGGAGGGCGGCGGCGGCGGCGGCGGCGGGGGUGUGGGGUCCUUCCCCCGCCCCCCCCCCCACGCCUCCUCCCCUCCUCCCGCCCACGCCCCGCUCCCCGCCCCCGGAGCCCCGCGGACGCUACGCCGCGACGAGUAGGAGGGCCGCUGCGGUGAGCCUUGAAGCCUAGGGCGCGGGCCCGGGUGGAGCCGCCGCAGGUGCAGAUCUUGGUGGUAGUAGCAAAUAUUCAAACGAGAACUUUGAAGGCCGAAGUGGAGAAGGGUUCCAUGUGAACAGCAGUUGAACAUGGGUCAGUCGGUCCUGAGAGAUGGGCGAGCGCCGUUCCGAAGGGACGGGCGAUGGCCUCCGUUGCCCUCGGCCGAUCGAAAGGGAGUCGGGUUCAGAUCCCCGAAUCCGGAGUGGCGGAGAUGGGCGCCGCGAGGCGUCCAGUGCGGUAACGCGACCGAUCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGUUCUCUUUUCUUUGUGAAGGGCAGGGCGCCCUGGAAUGGGUUCGCCCCGAGAGAGGGGCCCGUGCCUUGGAAAGCGUCGCGGUUCCGGCGGCGUCCGGUGAGCUCUCGCUGGCCCUUGAAAAUCCGGGGGAGAGGGUGUAAAUCUCGCGCCGGGCCGUACCCAUAUCCGCAGCAGGUCUCCAAGGUGAACAGCCUCUGGCAUGUUGGAACAAUGUAGGUAAGGGAAGUCGGCAAGCCGGAUCCGUAACUUCGGGAUAAGGAUUGGCUCUAAGGGCUGGGUCGGUCGGGCUGGGGCGCGAAGCGGGGCUGGGCGCGCGCCGCGGCUGGACGAGGCGCGCGCCCCCCCCACGCCCGGGGCACCCCCCUCGCGGCCCUCCCCCGCCCCACCCGCGCGCGCCGCUCGCUCCCUCCCCACCCCGCGCCCUCUCUCUCUCUCUCUCCCCCGCUCCCCGUCCUCCCCCCUCCCCGGGGGAGCGCCGCGUGGGGGCGCGGCGGGGGGAGAAGGGUCGGGGCGGCAGGGGCCGCGCGGCGGCCGCCGGGGCGGCCGGCGGGGGCAGGUCCCCGCGAGGGGGGCCCCGGGGACCCGGGGGGCCGGCGGCGGCGCGGACUCUGGACGCGAGCCGGGCCCUUCCCGUGGAUCGCCCCAGCUGCGGCGGGCGUCGCGGCCGCCCCCGGGGAGCCCGGCGGCGGCGCGGCGCGCCCCCCACCCCCACCCCACGUCUCGGUCGCGCGCGCGUCCGCUGGGGGCGGGAGCGGUCGGGCGGCGGCGGUCGGCGGGCGGCGGGGCGGGGCGGUUCGUCCCCCCGCCCUACCCCCCCGGCCCCGUCCGCCCCCCGUUCCCCCCUCCUCCUCGGCGCGCGGCGGCGGCGGCGGCAGGCGGCGGAGGGGCCGCGGGCCGGUCCCCCCCGCCGGGUCCGCCCCCGGGGCCGCGGUUCCGCGCGCGCCUCGCCUCGGCCGGCGCCUAGCAGCCGACUUAGAACUGGUGCGGACCAGGGGAAUCCGACUGUUUAAUUAAAACAAAGCAUCGCGAAGGCCCGCGGCGGGUGUUGACGCGAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAUUCAAUGAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUGAACGAGAUUCCCACUGUCCCUACCUACUAUCCAGCGAAACCACAGCCAAGGGAACGGGCUUGGCGGAAUCAGCGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAGUCUGGCACGGUGAAGAGACAUGAGAGGUGUAGAAUAAGUGGGAGGCCCCCGGCGCCCCCCCGGUGUCCCCGCGAGGGGCCCGGGGCGGGGUCCGCGGCCCUGCGGGCCGCCGGUGAAAUACCACUACUCUGAUCGUUUUUUCACUGACCCGGUGAGGCGGGGGGGCGAGCCCGAGGGGCUCUCGCUUCUGGCGCCAAGCGCCCGCCCGGCCGGGCGCGACCCGCUCCGGGGACAGUGCCAGGUGGGGAGUUUGACUGGGGCGGUACACCUGUCAAACGGUAACGCAGGUGUCCUAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUACGAAUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAGGUGUCAGAAAAGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUCCUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCGCCAAGCGUUGGAUUGUUCACCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCAGGUUCAGACAUUUGGUGUAUGUGCUUGGCUGAGGAGCCAAUGGGGCGAAGCUACCAUCUGUGGGAUUAUGACUGAACGCCUCUAAGUCAGAAUCCCGCCCAGGCGAACGAUACGGCAGCGCCGCGGAGCCUCGGUUGGCCUCGGAUAGCCGGUCCCCCGCCUGUCCCCGCCGGCGGGCCGCCCCCCCCUCCACGCGCCCCGCCGCGGGAGGGCGCGUGCCCCGCCGCGCGCCGGGACCGGGGUCCGGUGCGGAGUGCCCUUCGUCCUGGGAAACGGGGCGCGGCCGGAAAGGCGGCCGCCCCCUCGCCCGUCACGCACCGCACGUUCGUGGGGAACCUGGCGCUAAACCAUUCGUAGACGACCUGCUUCUGGGUCGGGGUUUCGUACGUAGCAGAGCAGCUCCCUCGCUGCGAUCUAUUGAAAGUCAGCCCUCGACACAAGGGUUUGUC
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnasnoop_input1b.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnasnoop_input1b.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,2 @@
+>ACA51
+AACCTACCCCATATACACCTCAGCTCAGGCCCTGTGCCTGGTCTGTATTGTGAATGGGGGAACATAG
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnasnoop_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnasnoop_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>ACA51
+>homo
+<<<<<<.|.<<<.<<<&(.>>>.>>>.((.((((...............................)))).))>>>>>>...).. 807,822;814 :   4,62  (-33.20 = -13.20 + -11.90 + -11.60 + -0.60 + 4.1 ) (-23.60) 
+UCCUCCCUCGGGAGGG&AACCUACCCCAUAUACACCUCAGCUCAGGCCCUGUGCCUGGUCUGUAUUGUGAAUGGGGGAACAUAG
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnasubopt_input1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnasubopt_input1.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnasubopt_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnasubopt_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,10 @@
+> Anolis_carolinensis_chrUn_GL343590.trna2-A [100]
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA  -2190    100
+(((((((..((((........)))).(((((.......))))).....(((((.......))))))))).))) -21.70
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). -21.20
+.(((((...((((........)))).(((((.......))))).....(((((.......))))).))))).. -20.90
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. -21.90
+> Anolis_carolinensis_chrUn_GL343207.trna3-A [100]
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA  -2870    100
+((((((...((((........)))).(((((.......))))).....(((((.......))))).)))))). -27.70
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). -28.70
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaup_input1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaup_input1.fa	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaup_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaup_result1.txt	Mon Feb 09 13:26:11 2015 -0500
@@ -0,0 +1,6 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC
+  55,  58 	 (0.021) 	 for u=  4
+RNAup output in file: Anolis_carolinensis_chrUn_GL343590.trna2-A_u1.out
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC
+  16,  19 	 (0.003) 	 for u=  4
+RNAup output in file: Anolis_carolinensis_chrUn_GL343207.trna3-A_u1.out
diff -r ec0fdb8c4ebb -r 5e58cbf27a05 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Feb 04 12:45:16 2015 -0500
+++ b/tool_dependencies.xml	Mon Feb 09 13:26:11 2015 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="vienna_rna" version="2.1">
-        <repository changeset_revision="276d1f7a4d05" name="package_vienna_rna_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="3b53eda26527" name="package_vienna_rna_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>