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changeset 0:09e921a25c68 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
author yhoogstrate
date Mon, 03 Aug 2015 08:28:39 -0400
parents
children 27f670a42ba2
files README.rst segmentation-fold.xml test-data/test_01.dbn test-data/test_01.fa test-data/test_02.dbn test-data/test_02.fa test-data/test_03.dbn test-data/test_03.fa test-data/test_04.dbn test-data/test_04.fa test-data/test_05.dbn test-data/test_05.fa test-data/test_06.dbn test-data/test_06.fa test-data/test_07.dbn test-data/test_07.fa test-data/test_08.dbn test-data/test_08.fa test-data/test_09.dbn test-data/test_09.fa test-data/test_10.dbn test-data/test_10.fa test-data/test_11.dbn test-data/test_11.fa test-data/test_12.dbn test-data/test_12.fa test-data/test_13.dbn test-data/test_13.fa test-data/test_14.dbn test-data/test_14.fa test-data/test_15.dbn test-data/test_15.fa test-data/test_16.dbn test-data/test_16.fa test-data/test_17.dbn test-data/test_17.fa test-data/test_18.dbn test-data/test_18.fa test-data/test_19.dbn test-data/test_19.fa test-data/test_20.dbn test-data/test_20.fa test-data/test_21.dbn test-data/test_21.fa test-data/test_22.dbn test-data/test_22.fa test-data/test_23.dbn test-data/test_23.fa test-data/test_24.dbn test-data/test_24.fa test-data/test_25.dbn test-data/test_25.fa test-data/test_26.dbn test-data/test_26.fa test-data/test_27.dbn test-data/test_27.fa test-data/test_28.dbn test-data/test_28.fa tool_dependencies.xml
diffstat 59 files changed, 387 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,31 @@
+Segmentation-fold wrapper for Galaxy
+====================================
+
+https://github.com/yhoogstrate/segmentation-fold
+
+Segmentation-fold: An algorithm for predicting RNA 2D structures including K-turns
+
+Development
+-----------
+
+* Repository-Maintainer: Youri Hoogstrate
+* Repository-Developers: Youri Hoogstrate
+
+* Repository-Development: https://github.com/ErasmusMC-Bioinformatics/galaxy-tools
+
+The tool wrapper has been written by Youri Hoogstrate as MSc research
+assignment at Technical University of Delft and University of Leiden.
+
+License
+-------
+
+**segmentation-fold** and **wrapper**:
+
+GPL (>=3)
+
+References
+----------
+Segmentaton-fold was formerly known as yh-kt-fold and the corresponding
+thesis can be found at the following url:
+
+https://yh-kt-fold.googlecode.com/files/Report.pdf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/segmentation-fold.xml	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,210 @@
+<tool id="segmentation_fold" name="segmentation-fold" version="0.2.0">
+    <description>RNA-Folding including predefined segments including K-turns</description>
+    
+    <requirements>
+        <requirement type="package" version="1.0.0">segmentation-fold</requirement>
+    </requirements>
+    
+    <stdio></stdio>
+    
+    <version_command>segmentation-fold -V | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</version_command>
+    
+    <command><![CDATA[
+        segmentation-fold
+            
+            #if $input.method == "fasta"
+                -f $input.input_fasta
+            #else
+                -s $input.input_sequence
+            #end if
+            
+            -p $predict_segments
+            -h $min_hairpin_size
+            
+            #if $parameters.settings == "default"
+                -x "${SEGMENTATION_FOLD_DEFAULT_XML}"
+            #else
+                -x $parameters.input_xml
+            #end if
+            
+            -t \${GALAXY_SLOTS:-2}
+            > $output_dbn
+    ]]></command>
+    
+    <inputs>
+        
+        <conditional name="input">
+            <param name="method" type="select" label="Energy parameters">
+                <option value="fasta" selected="true">As FASTA-file</option>
+                <option value="text">As text</option>
+            </param>
+            <when value="fasta">
+                <param name="input_fasta" type="data" format="fasta" label="Fasta file with RNA-sequece (-f)" />
+            </when>
+            <when value="text"> 
+                <param name="input_sequence" type="text" label="RNA-sequece (-s)" />
+            </when>
+        </conditional>
+        
+        <param name="predict_segments" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Enable segment prediction functionality (-p)" />
+        <param name="min_hairpin_size" type="integer" min="1" value="3" label="Minimum hairpin size (-h)" />
+        
+        <conditional name="parameters">
+            <param name="settings" type="select" label="Energy parameters">
+                <option value="default" selected="true">Default</option>
+                <option value="custom">Custom</option>
+            </param>
+            <when value="default" />
+            <when value="custom"> 
+                <param name="input_xml" type="data" format="xml" multiple="false" label="Use custom 'segments.xml'-syntaxed file (-x)" />
+            </when>
+        </conditional>
+    </inputs>
+    
+    <outputs>
+        <data format="dot-bracket" name="output_dbn" label="${tool.name} on ${input.input_fasta.hid + ': ' + input.input_fasta.name if $input.method == 'fasta' else $input.input_sequence.upper() }" />
+    </outputs>
+    
+    <tests>
+        <test>
+            <param  name="input_fasta" value="test_01.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_01.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_02.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_02.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_03.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_03.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_04.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_04.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_05.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_05.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_06.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_06.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_07.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_07.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_08.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_08.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_09.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_09.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_10.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_10.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_11.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_11.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_12.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_12.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_13.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_13.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_14.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_14.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_15.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_15.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_16.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_16.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_17.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_17.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_18.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_18.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_19.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_19.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_20.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_20.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_21.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_21.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_22.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_22.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_23.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_23.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_24.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_24.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_25.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_25.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_26.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_26.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_27.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_27.dbn" />
+        </test>
+        <test>
+            <param  name="input_fasta" value="test_28.fa" ftype="fasta" />
+            <output name="output_dbn"   file="test_28.dbn" />
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+Segmentation-fold is a bioinformatics application that predicts RNA
+2D-structure with an extended version of the Zuker algorithm. This
+modification contains a new "structure element" named a segment and is
+capable of folding a pre-defined substructure with multiple canonical
+or non-canonical pairings.
+
+This allows folding of more complex structures like the K-turns, which
+are also part of the implemented free energy tables. These thermodynamic
+parameters (free Gibbs energy levels) have been estimated using a
+computational approach and therefore lack accuracy.
+    ]]></help>
+    
+    <citations>
+        <citation type="bibtex">
+           @mastersthesis{mastersthesis,
+              author       = {Youri Hoogstrate}, 
+              title        = {An algorithm for predicting RNA 2D structures including K-turns},
+              school       = {University of Technology Delft, Leiden University},
+              year         = 2012,
+              address      = {},
+              month        = 11,
+              note         = {Research assignment for Master Computer-science},
+              url          = { https://yh-kt-fold.googlecode.com/files/Report.pdf }
+            }
+        </citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_01.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 34bp, dE: -32.2572 kcal/mole
+CCAUGGGGAGCCGCACGGAGGCGAAGAACCAUGG
+((((((((((((.......)))...)))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_01.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-7
+CCAUGGGGAGCCGCACGGAGGCGAAGAACCAUGG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_02.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 34bp, dE: -34.4572 kcal/mole
+CCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGG
+((((((((((((..(...))))...)))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_02.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-7
+CCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_03.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 35bp, dE: -31.2572 kcal/mole
+CGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCG
+((((((((((((..(...)))))....))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_03.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-7
+CGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_04.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 34bp, dE: -30.4872 kcal/mole
+CCCCGACGAGCUGGAGAUACCCUUUGACUCGGGG
+((((((((((..((.....)))...)))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_04.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-7
+CCCCGACGAGCUGGAGAUACCCUUUGACUCGGGG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_05.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 47bp, dE: -42.9072 kcal/mole
+CCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGG
+((((.(((((..(((((.((((....))))))))))))...))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_05.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 16S rRNA containing Kt-11
+CCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_06.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 47bp, dE: -41.3572 kcal/mole
+GGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCC
+((((.(((((..((((((.(((....))))))))))))...))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_06.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 16S rRNA containing Kt-11
+GGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_07.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 31bp, dE: -28.7072 kcal/mole
+AACCGAAGCCCUCACGGGCAAUGUGGUGUCA
+.((((.(((((....))))...)))))....
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_07.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-15
+AACCGAAGCCCUCACGGGCAAUGUGGUGUCA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_08.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 37bp, dE: -33.7572 kcal/mole
+UUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAG
+((((((((((((((.(...))))...)))))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_08.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 16S rRNA containing Kt-23
+UUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_09.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 37bp, dE: -30.8072 kcal/mole
+UUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAG
+((((((((((((((.(...))))...)))))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_09.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 16S rRNA containing Kt-23
+UUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_10.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 109bp, dE: -82.9072 kcal/mole
+CUCCGCCGAGGUAGUCUGUGAGGUAGAGCGACCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAGACGCCGUUUGACGCGGGG
+((((((((((((.(((((((((((.((((.(((....))))).)).))))).(((.(((((.((((....))))..)))))...))))))))))))....)))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_10.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-38
+CUCCGCCGAGGUAGUCUGUGAGGUAGAGCGACCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAGACGCCGUUUGACGCGGGG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_11.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 53bp, dE: -49.0072 kcal/mole
+GGUGGUCUCGAGCCCUAGACAGCCGGUUUUUUCCGGCCGAGGUUUGAGGCGCC
+(((.((((((((((...((.((((((......)))))))))))))))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_11.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-42
+GGUGGUCUCGAGCCCUAGACAGCCGGUUUUUUCCGGCCGAGGUUUGAGGCGCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_12.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 53bp, dE: -51.5072 kcal/mole
+GGAUGUGGCGCCGCGAAGACAGCCAGUUUUUUCUGGUCGAGUGGCGCCGCGCC
+((.(((((((((((...((.((((((......)))))))))))))))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_12.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-42
+GGAUGUGGCGCCGCGAAGACAGCCAGUUUUUUCUGGUCGAGUGGCGCCGCGCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_13.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 53bp, dE: -44.8072 kcal/mole
+GGAUGUGUCGUCGCAUAGACAGCCAGUUUUUUCUGGUCGAGUGACGAUGCGCC
+((.(((((((((((...((.((((((......)))))))))))))))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_13.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-42
+GGAUGUGUCGUCGCAUAGACAGCCAGUUUUUUCUGGUCGAGUGACGAUGCGCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_14.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 53bp, dE: -39.2072 kcal/mole
+CGAUGUGGGAAGGCCCAGACAGCCAGUUUUUUCUGGUCGAGUCGGCCUGCGCG
+((.((..((..(((...((.((((((......)))))))))))..))..))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_14.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-42
+CGAUGUGGGAAGGCCCAGACAGCCAGUUUUUUCUGGUCGAGUCGGCCUGCGCG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_15.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 49bp, dE: -37.8572 kcal/mole
+CUCUAAUUGGAUGGAAGUAGGGGUGAAAACUCCUAUGGACCGAUUAGUG
+(.((((((((...(((((((((((....))))))))))))))))))).)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_15.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-46
+CUCUAAUUGGAUGGAAGUAGGGGUGAAAACUCCUAUGGACCGAUUAGUG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_16.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 50bp, dE: -44.4072 kcal/mole
+UUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGCGGCUGGAGGUAAGGGAA
+(((((..((((...((((((((.((.....)))))))))))))).)))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_16.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-46
+UUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGCGGCUGGAGGUAAGGGAA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_17.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 49bp, dE: -38.8072 kcal/mole
+UUCAGUCCGCGGUGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAA
+(((((((.((...((((((((.((....)).)))))))))).)))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_17.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-46
+UUCAGUCCGCGGUGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_18.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 50bp, dE: -37.7072 kcal/mole
+UUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAA
+(((((.(.(((...(((((((((((....)))))))))))))).))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_18.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-46
+UUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_19.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 30bp, dE: -29.8572 kcal/mole
+UCCGUGGAAGCCGUAAUGGCAGGAAGCGGA
+((((((((.((((...))))..))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_19.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial 23S rRNA containing Kt-58
+UCCGUGGAAGCCGUAAUGGCAGGAAGCGGA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_20.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 22bp, dE: -23.2072 kcal/mole
+GCCAAUGAGGUUUAUCCGAGGC
+(((...((((.....)))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_20.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial U4 snRNA (small)
+GCCAAUGAGGUUUAUCCGAGGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_21.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 34bp, dE: -30.6072 kcal/mole
+ACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGU
+(((((.(((...(((((....)))))))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_21.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Partial U4 snRNA (large)
+ACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGU
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_22.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 25bp, dE: -24.4072 kcal/mole
+GCUCUGACCGAAAGGCGUGAUGAGC
+(((((((((....))...)))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_22.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>C/D-box snoRNA
+GCUCUGACCGAAAGGCGUGAUGAGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_23.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 85bp, dE: -70.7144 kcal/mole
+GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC
+((((((((...(((((((.((...(..(((((((((((((.....))))))))...)))))..)))))....)))))))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_23.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>Artificial double C/D K-turn construct
+GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_24.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 34bp, dE: -29.0072 kcal/mole
+GGACGCAGAGAUGGUCUUUUUGACCGGAGUGUCC
+((((((...(((((((.....)))))))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_24.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>L30e pre-mRNA
+GGACGCAGAGAUGGUCUUUUUGACCGGAGUGUCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_25.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 26bp, dE: -24.7072 kcal/mole
+GGUGGAGGGACUGGCCCGAUGAAACC
+(((((((((.....)))...))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_25.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>SAM riboswitch operon
+GGUGGAGGGACUGGCCCGAUGAAACC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_26.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 55bp, dE: -43.9072 kcal/mole
+GGGAGUAAAGAUUGAGACAAGUAGGACUUCGGUCCGAAUACACUCAUGAACUCCC
+((((((...(((((((....(((((((....))))...))).)))))))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_26.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>T box
+GGGAGUAAAGAUUGAGACAAGUAGGACUUCGGUCCGAAUACACUCAUGAACUCCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_27.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 36bp, dE: -26.2072 kcal/mole
+AACAAUGAUGAAUGGGUUUUUUACUCAUUUUGAGUU
+(((...(((((((((((.....))))))))))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_27.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>c-di-GMP-II aptamer
+AACAAUGAUGAAUGGGUUUUUUACUCAUUUUGAGUU
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_28.dbn	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,3 @@
+>Sequence length: 26bp, dE: -24.7072 kcal/mole
+GGUGAAGGGACUGGCCCGACGAAACC
+(((((((((.....)))...))))))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_28.fa	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,2 @@
+>G2nA SAM riboswitch
+GGUGAAGGGACUGGCCCGACGAAACC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Aug 03 08:28:39 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="segmentation-fold" version="1.0.0">
+        <repository changeset_revision="f4fce0d27352" name="package_segmentation_fold_1_0_0" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>