# HG changeset patch
# User yhoogstrate
# Date 1449130928 18000
# Node ID 27f670a42ba27ac2acd775cc24aa433c82baf096
# Parent  09e921a25c681877c91005bc9e152277c3d3fd10
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 4f43c60fd8d3827382fa55c7b6174fa925d7f8e7

diff -r 09e921a25c68 -r 27f670a42ba2 segmentation-fold.xml
--- a/segmentation-fold.xml	Mon Aug 03 08:28:39 2015 -0400
+++ b/segmentation-fold.xml	Thu Dec 03 03:22:08 2015 -0500
@@ -1,13 +1,13 @@
-<tool id="segmentation_fold" name="segmentation-fold" version="0.2.0">
+<tool id="segmentation_fold" name="segmentation-fold" version="1.1.0_1">
     <description>RNA-Folding including predefined segments including K-turns</description>
     
     <requirements>
-        <requirement type="package" version="1.0.0">segmentation-fold</requirement>
+        <requirement type="package" version="1.1.0">segmentation-fold</requirement>
     </requirements>
     
     <stdio></stdio>
     
-    <version_command>segmentation-fold -V | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</version_command>
+    <version_command>segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</version_command>
     
     <command><![CDATA[
         segmentation-fold
@@ -22,17 +22,16 @@
             -h $min_hairpin_size
             
             #if $parameters.settings == "default"
-                -x "${SEGMENTATION_FOLD_DEFAULT_XML}"
+                -x "\$SEGMENTATION_FOLD_DEFAULT_XML"
             #else
-                -x $parameters.input_xml
+                -x "${parameters.input_xml}"
             #end if
             
-            -t \${GALAXY_SLOTS:-2}
+            -t \${GALAXY_SLOTS:-4}
             > $output_dbn
     ]]></command>
     
     <inputs>
-        
         <conditional name="input">
             <param name="method" type="select" label="Energy parameters">
                 <option value="fasta" selected="true">As FASTA-file</option>
@@ -62,7 +61,8 @@
     </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 $input.input_sequence.upper() }" />
+        <data format="dot-bracket" name="output_dbn" label="asdasdasd" />
+        <!--<data format="dot-bracket" name="output_dbn" label="${tool.name} on ${str(input.input_fasta.hid) + ': ' + input.input_fasta.name if $input.method == 'fasta' else $input.input_sequence.upper() }" />-->
     </outputs>
     
     <tests>
@@ -184,13 +184,13 @@
 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
+capable of folding a pre-defined substructures 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.
+This allows folding of more complex structures like K-turns, which are
+also part of the implemented free energy table. These thermodynamic
+parameters (free Gibbs energy) have been estimated using a in silico
+approach and therefore lack high resolution.
     ]]></help>
     
     <citations>
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_02.dbn
--- a/test-data/test_02.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_02.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
 >Sequence length: 34bp, dE: -34.4572 kcal/mole
 CCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGG
-((((((((((((..(...))))...)))))))))
+((((((((((((.......)))...)))))))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_03.dbn
--- a/test-data/test_03.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_03.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
 >Sequence length: 35bp, dE: -31.2572 kcal/mole
 CGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCG
-((((((((((((..(...)))))....))))))))
+((((((((((((.......))))....))))))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_05.dbn
--- a/test-data/test_05.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_05.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
->Sequence length: 47bp, dE: -42.9072 kcal/mole
+>Sequence length: 47bp, dE: -42.5072 kcal/mole
 CCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGG
-((((.(((((..(((((.((((....))))))))))))...))))))
+((((.(((((..((((((((.......)))))))))))...))))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_06.dbn
--- a/test-data/test_06.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_06.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
->Sequence length: 47bp, dE: -41.3572 kcal/mole
+>Sequence length: 47bp, dE: -40.3572 kcal/mole
 GGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCC
-((((.(((((..((((((.(((....))))))))))))...))))))
+((((.(((((..((((((((.......)))))))))))...))))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_07.dbn
--- a/test-data/test_07.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_07.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
->Sequence length: 31bp, dE: -28.7072 kcal/mole
+>Sequence length: 31bp, dE: -26.5072 kcal/mole
 AACCGAAGCCCUCACGGGCAAUGUGGUGUCA
-.((((.(((((....))))...)))))....
+..(((.(((((....))))...)))).....
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_08.dbn
--- a/test-data/test_08.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_08.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
 >Sequence length: 37bp, dE: -33.7572 kcal/mole
 UUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAG
-((((((((((((((.(...))))...)))))))))))
+((((((((((((((......)))...)))))))))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_09.dbn
--- a/test-data/test_09.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_09.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
 >Sequence length: 37bp, dE: -30.8072 kcal/mole
 UUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAG
-((((((((((((((.(...))))...)))))))))))
+((((((((((((((......)))...)))))))))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_10.dbn
--- a/test-data/test_10.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_10.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
->Sequence length: 109bp, dE: -82.9072 kcal/mole
+>Sequence length: 109bp, dE: -76.7072 kcal/mole
 CUCCGCCGAGGUAGUCUGUGAGGUAGAGCGACCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAGACGCCGUUUGACGCGGGG
-((((((((((((.(((((((((((.((((.(((....))))).)).))))).(((.(((((.((((....))))..)))))...))))))))))))....)))))))))
+((((((((((((.(((((((((...(((.(((..(..((((((.(((.((((....)))).)))))))))))))...)))....))))))))))))....)))))))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_11.dbn
--- a/test-data/test_11.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_11.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -49.0072 kcal/mole
+>Sequence length: 53bp, dE: -46.6072 kcal/mole
 GGUGGUCUCGAGCCCUAGACAGCCGGUUUUUUCCGGCCGAGGUUUGAGGCGCC
-(((.((((((((((...((.((((((......)))))))))))))))))))))
+((((.(((((((((...((.((((((......)))))))))))))))))))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_12.dbn
--- a/test-data/test_12.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_12.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -51.5072 kcal/mole
+>Sequence length: 53bp, dE: -50.2072 kcal/mole
 GGAUGUGGCGCCGCGAAGACAGCCAGUUUUUUCUGGUCGAGUGGCGCCGCGCC
 ((.(((((((((((...((.((((((......)))))))))))))))))))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_13.dbn
--- a/test-data/test_13.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_13.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -44.8072 kcal/mole
+>Sequence length: 53bp, dE: -43.5072 kcal/mole
 GGAUGUGUCGUCGCAUAGACAGCCAGUUUUUUCUGGUCGAGUGACGAUGCGCC
 ((.(((((((((((...((.((((((......)))))))))))))))))))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_14.dbn
--- a/test-data/test_14.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_14.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -39.2072 kcal/mole
+>Sequence length: 53bp, dE: -37.9072 kcal/mole
 CGAUGUGGGAAGGCCCAGACAGCCAGUUUUUUCUGGUCGAGUCGGCCUGCGCG
 ((.((..((..(((...((.((((((......)))))))))))..))..))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_16.dbn
--- a/test-data/test_16.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_16.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
->Sequence length: 50bp, dE: -44.4072 kcal/mole
+>Sequence length: 50bp, dE: -43.4072 kcal/mole
 UUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGCGGCUGGAGGUAAGGGAA
-(((((..((((...((((((((.((.....)))))))))))))).)))))
+(((((...(((...((((((((..((....)))))))))))))..)))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_17.dbn
--- a/test-data/test_17.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_17.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
->Sequence length: 49bp, dE: -38.8072 kcal/mole
+>Sequence length: 49bp, dE: -37.3072 kcal/mole
 UUCAGUCCGCGGUGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAA
 (((((((.((...((((((((.((....)).)))))))))).)))))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_18.dbn
--- a/test-data/test_18.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_18.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
 >Sequence length: 50bp, dE: -37.7072 kcal/mole
 UUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAA
-(((((.(.(((...(((((((((((....)))))))))))))).))))))
+(((((...(((...(((((((((((....))))))))))))))..)))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_19.dbn
--- a/test-data/test_19.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_19.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
->Sequence length: 30bp, dE: -29.8572 kcal/mole
+>Sequence length: 30bp, dE: -28.4572 kcal/mole
 UCCGUGGAAGCCGUAAUGGCAGGAAGCGGA
-((((((((.((((...))))..))))))))
+((((((((.(((.....)))..))))))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_21.dbn
--- a/test-data/test_21.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_21.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
->Sequence length: 34bp, dE: -30.6072 kcal/mole
+>Sequence length: 34bp, dE: -27.7072 kcal/mole
 ACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGU
 (((((.(((...(((((....)))))))))))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_23.dbn
--- a/test-data/test_23.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_23.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
->Sequence length: 85bp, dE: -70.7144 kcal/mole
+>Sequence length: 85bp, dE: -70.4144 kcal/mole
 GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC
-((((((((...(((((((.((...(..(((((((((((((.....))))))))...)))))..)))))....)))))))))))))
+((((((((...(((((..(((......(((((((((((((.....))))))))...)))))...))).....)))))))))))))
diff -r 09e921a25c68 -r 27f670a42ba2 test-data/test_26.dbn
--- a/test-data/test_26.dbn	Mon Aug 03 08:28:39 2015 -0400
+++ b/test-data/test_26.dbn	Thu Dec 03 03:22:08 2015 -0500
@@ -1,3 +1,3 @@
->Sequence length: 55bp, dE: -43.9072 kcal/mole
+>Sequence length: 55bp, dE: -42.1072 kcal/mole
 GGGAGUAAAGAUUGAGACAAGUAGGACUUCGGUCCGAAUACACUCAUGAACUCCC
 ((((((...(((((((....(((((((....))))...))).)))))))))))))
diff -r 09e921a25c68 -r 27f670a42ba2 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Aug 03 08:28:39 2015 -0400
+++ b/tool_dependencies.xml	Thu Dec 03 03:22:08 2015 -0500
@@ -1,6 +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 name="segmentation-fold" version="1.1.0">
+        <repository changeset_revision="2c69127ea0cd" name="package_segmentation_fold_1_1_0" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>