# HG changeset patch
# User yhoogstrate
# Date 1463646689 14400
# Node ID 63156f020cd3cdc7ee4c4dd05c7066b7c60bba67
# Parent  c690aa928d3daa9c4d7d267d125542493e0f1ac9
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit fb0bbb26638c0185ef16efa2e0ac3952d671b711-dirty

diff -r c690aa928d3d -r 63156f020cd3 macros.xml
--- a/macros.xml	Fri May 06 06:08:36 2016 -0400
+++ b/macros.xml	Thu May 19 04:31:29 2016 -0400
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">smf-v1.6-4_utils-v1.0.3</token>
+    <token name="@VERSION@">smf-v1.6-5_utils-v1.0.3</token>
 
     <xml name="stdio">
         <stdio>
@@ -13,12 +13,14 @@
 
 
     <token name="@REQUIREMENTS_UTILS@"><![CDATA[
+        <requirement type="package" version="2.7.10">python</requirement>
+        <requirement type="package" version="1.9">numpy</requirement>
+        <requirement type="package" version="0.8.2.1">pysam</requirement>
         <requirement type="package" version="1.0.3">segmentation-fold-utils</requirement>
-        <requirement type="package" version="2.7.10">python</requirement>
     ]]></token>
 
     <token name="@REQUIREMENTS_SMF@"><![CDATA[
-        <requirement type="package" version="1.6.3">segmentation-fold</requirement>
+        <requirement type="package" version="1.6.5">segmentation-fold</requirement>
     ]]></token>
 
 
diff -r c690aa928d3d -r 63156f020cd3 segmentation-fold.xml
--- a/segmentation-fold.xml	Fri May 06 06:08:36 2016 -0400
+++ b/segmentation-fold.xml	Thu May 19 04:31:29 2016 -0400
@@ -1,6 +1,6 @@
 <tool id="segmentation_fold" name="segmentation-fold" version="@VERSION@-1">
     <description>RNA-Folding including predefined segments including K-turns</description>
-	<macros>
+    <macros>
         <import>macros.xml</import>
     </macros>
     
diff -r c690aa928d3d -r 63156f020cd3 test-data/DBNFile.test_03.in.dbn
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DBNFile.test_03.in.dbn	Thu May 19 04:31:29 2016 -0400
@@ -0,0 +1,42 @@
+>chr3.rna:5-35(+) x Kt-CD-box.CGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGT
+>chr3.rna:5-35(+) x Kt-CD-box.UGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGT
+(((.(((........))).)))........	.((...(((((...........))))))).	-13.125
+>chr3.rna:5-80(+) x Kt-CD-box.CGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA
+>chr3.rna:5-80(+) x Kt-CD-box.UGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA
+(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))	(((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))	0.0
+(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))	(((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))	0.0
+>chr3.rna:50-80(+) x Kt-CD-box.CGU
+ACTTGTGATGAAACACTCATGGTCTGAAGA
+>chr3.rna:50-80(+) x Kt-CD-box.UGU
+ACTTGTGATGAAACACTCATGGTCTGAAGA
+..(..(((((...)).)))..)........	.((...(((((....(....).))))))).	-13.125
+>chr4_SNORD118_revised:1-74(+) x Kt-CD-box.CGU
+GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTG
+...((............(((((.((.((((.....)))).))))))).((((((...........))))))))	...((..((((((............))...)))).(((......))).((((((...........))))))))	0.0
+>chr4_SNORD118_revised:1-74(+) x Kt-CD-box.UGU
+GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTG
+>chr4_SNORD118_revised:1-88(+) x Kt-CD-box.CGU
+GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTGCTCCTGTCTGATTT
+.........(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))......	..(((..((((((............))...))))...........(((((((((...........)))))))))...))).......	0.0
+>chr4_SNORD118_revised:1-88(+) x Kt-CD-box.UGU
+GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTGCTCCTGTCTGATTT
+>chr3.rna.RC:35-5(-) x Kt-CD-box.CGU
+ACTTGTGATGAAACACTCATGGTCTGAAGA
+>chr3.rna.RC:35-5(-) x Kt-CD-box.UGU
+ACTTGTGATGAAACACTCATGGTCTGAAGA
+..(..(((((...)).)))..)........	.((...(((((....(....).))))))).	-13.125
+>chr3.rna.RC:80-5(-) x Kt-CD-box.CGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA
+>chr3.rna.RC:80-5(-) x Kt-CD-box.UGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA
+(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))	(((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))	0.0
+(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))	(((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))	0.0
+>chr3.rna.RC:80-50(-) x Kt-CD-box.CGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGT
+>chr3.rna.RC:80-50(-) x Kt-CD-box.UGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGT
+(((.(((........))).)))........	.((...(((((...........))))))).	-13.125
diff -r c690aa928d3d -r 63156f020cd3 test-data/DBNFile.test_03.out.l.dbn
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DBNFile.test_03.out.l.dbn	Thu May 19 04:31:29 2016 -0400
@@ -0,0 +1,14 @@
+>chr3.rna:5-80(+) x Kt-CD-box.UGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA
+(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))	(((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))	0.0
+(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))	(((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))	0.0
+>chr4_SNORD118_revised:1-74(+) x Kt-CD-box.CGU
+GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTG
+...((............(((((.((.((((.....)))).))))))).((((((...........))))))))	...((..((((((............))...)))).(((......))).((((((...........))))))))	0.0
+>chr4_SNORD118_revised:1-88(+) x Kt-CD-box.CGU
+GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTGCTCCTGTCTGATTT
+.........(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))......	..(((..((((((............))...))))...........(((((((((...........)))))))))...))).......	0.0
+>chr3.rna.RC:80-5(-) x Kt-CD-box.UGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA
+(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))	(((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))	0.0
+(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))	(((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))	0.0
diff -r c690aa928d3d -r 63156f020cd3 test-data/DBNFile.test_03.out.s.dbn
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DBNFile.test_03.out.s.dbn	Thu May 19 04:31:29 2016 -0400
@@ -0,0 +1,28 @@
+>chr3.rna:5-35(+) x Kt-CD-box.CGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGT
+>chr3.rna:5-35(+) x Kt-CD-box.UGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGT
+(((.(((........))).)))........	.((...(((((...........))))))).	-13.125
+>chr3.rna:5-80(+) x Kt-CD-box.CGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA
+>chr3.rna:50-80(+) x Kt-CD-box.CGU
+ACTTGTGATGAAACACTCATGGTCTGAAGA
+>chr3.rna:50-80(+) x Kt-CD-box.UGU
+ACTTGTGATGAAACACTCATGGTCTGAAGA
+..(..(((((...)).)))..)........	.((...(((((....(....).))))))).	-13.125
+>chr4_SNORD118_revised:1-74(+) x Kt-CD-box.UGU
+GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTG
+>chr4_SNORD118_revised:1-88(+) x Kt-CD-box.UGU
+GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTGCTCCTGTCTGATTT
+>chr3.rna.RC:35-5(-) x Kt-CD-box.CGU
+ACTTGTGATGAAACACTCATGGTCTGAAGA
+>chr3.rna.RC:35-5(-) x Kt-CD-box.UGU
+ACTTGTGATGAAACACTCATGGTCTGAAGA
+..(..(((((...)).)))..)........	.((...(((((....(....).))))))).	-13.125
+>chr3.rna.RC:80-5(-) x Kt-CD-box.CGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA
+>chr3.rna.RC:80-50(-) x Kt-CD-box.CGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGT
+>chr3.rna.RC:80-50(-) x Kt-CD-box.UGU
+TCTTGTGATGAGAAGTACTGGATCTGAAGT
+(((.(((........))).)))........	.((...(((((...........))))))).	-13.125
diff -r c690aa928d3d -r 63156f020cd3 test-data/SNORD114-4-revised.scan-for-segments.txt
--- a/test-data/SNORD114-4-revised.scan-for-segments.txt	Fri May 06 06:08:36 2016 -0400
+++ b/test-data/SNORD114-4-revised.scan-for-segments.txt	Thu May 19 04:31:29 2016 -0400
@@ -1,12 +1,12 @@
->SNORD114-4 revised x Kt-7 G2nA SAM riboswitch H. marismortui
+>SNORD114-4 revised x Kt-7 G2nA SAM riboswitch (H. marismortui)
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-7 T. thermophilus
+>SNORD114-4 revised x Kt-7 (T. thermophilus)
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-7 E. coli
+>SNORD114-4 revised x Kt-7 (E. coli)
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-7 D. radiodurans
+>SNORD114-4 revised x Kt-7 (D. radiodurans)
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-11 T. thermophilus
+>SNORD114-4 revised x Kt-11 (T. thermophilus)
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 revised x Kt-11.eco
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
@@ -53,5 +53,5 @@
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 revised x Kt-c-di-GMP-II.cac
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-G2nA-SAM-riboswitch T. tengcongensi
+>SNORD114-4 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
diff -r c690aa928d3d -r 63156f020cd3 test-data/SNORD118-revised.scan-for-segments.txt
--- a/test-data/SNORD118-revised.scan-for-segments.txt	Fri May 06 06:08:36 2016 -0400
+++ b/test-data/SNORD118-revised.scan-for-segments.txt	Thu May 19 04:31:29 2016 -0400
@@ -1,12 +1,12 @@
->SNORD118 revised x Kt-7 G2nA SAM riboswitch H. marismortui
+>SNORD118 revised x Kt-7 G2nA SAM riboswitch (H. marismortui)
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-7 T. thermophilus
+>SNORD118 revised x Kt-7 (T. thermophilus)
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-7 E. coli
+>SNORD118 revised x Kt-7 (E. coli)
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-7 D. radiodurans
+>SNORD118 revised x Kt-7 (D. radiodurans)
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-11 T. thermophilus
+>SNORD118 revised x Kt-11 (T. thermophilus)
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 revised x Kt-11.eco
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
@@ -53,5 +53,5 @@
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 revised x Kt-c-di-GMP-II.cac
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-G2nA-SAM-riboswitch T. tengcongensi
+>SNORD118 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
diff -r c690aa928d3d -r 63156f020cd3 test-data/SNORD13-revised.scan-for-segments.txt
--- a/test-data/SNORD13-revised.scan-for-segments.txt	Fri May 06 06:08:36 2016 -0400
+++ b/test-data/SNORD13-revised.scan-for-segments.txt	Thu May 19 04:31:29 2016 -0400
@@ -1,12 +1,12 @@
->SNORD13 revised x Kt-7 G2nA SAM riboswitch H. marismortui
+>SNORD13 revised x Kt-7 G2nA SAM riboswitch (H. marismortui)
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-7 T. thermophilus
+>SNORD13 revised x Kt-7 (T. thermophilus)
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-7 E. coli
+>SNORD13 revised x Kt-7 (E. coli)
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-7 D. radiodurans
+>SNORD13 revised x Kt-7 (D. radiodurans)
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-11 T. thermophilus
+>SNORD13 revised x Kt-11 (T. thermophilus)
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 revised x Kt-11.eco
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
@@ -53,5 +53,5 @@
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 revised x Kt-c-di-GMP-II.cac
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-G2nA-SAM-riboswitch T. tengcongensi
+>SNORD13 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
diff -r c690aa928d3d -r 63156f020cd3 test-data/SNORD48-revised.scan-for-segments.txt
--- a/test-data/SNORD48-revised.scan-for-segments.txt	Fri May 06 06:08:36 2016 -0400
+++ b/test-data/SNORD48-revised.scan-for-segments.txt	Thu May 19 04:31:29 2016 -0400
@@ -1,56 +1,56 @@
->SNORD48 revised 2 extra bases on 5 end x Kt-7 G2nA SAM riboswitch H. marismortui
+>SNORD48 revised (2 extra bases on 5' end) x Kt-7 G2nA SAM riboswitch (H. marismortui)
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-7 T. thermophilus
+>SNORD48 revised (2 extra bases on 5' end) x Kt-7 (T. thermophilus)
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-7 E. coli
+>SNORD48 revised (2 extra bases on 5' end) x Kt-7 (E. coli)
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-7 D. radiodurans
+>SNORD48 revised (2 extra bases on 5' end) x Kt-7 (D. radiodurans)
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-11 T. thermophilus
+>SNORD48 revised (2 extra bases on 5' end) x Kt-11 (T. thermophilus)
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-11.eco
+>SNORD48 revised (2 extra bases on 5' end) x Kt-11.eco
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-15.hma
+>SNORD48 revised (2 extra bases on 5' end) x Kt-15.hma
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-23.tth
+>SNORD48 revised (2 extra bases on 5' end) x Kt-23.tth
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-23.eco
+>SNORD48 revised (2 extra bases on 5' end) x Kt-23.eco
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-38.hma
+>SNORD48 revised (2 extra bases on 5' end) x Kt-38.hma
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-42.hma
+>SNORD48 revised (2 extra bases on 5' end) x Kt-42.hma
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-42.tth
+>SNORD48 revised (2 extra bases on 5' end) x Kt-42.tth
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-42.dra
+>SNORD48 revised (2 extra bases on 5' end) x Kt-42.dra
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-42.eco
+>SNORD48 revised (2 extra bases on 5' end) x Kt-42.eco
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-46.hma
+>SNORD48 revised (2 extra bases on 5' end) x Kt-46.hma
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-46.tth
+>SNORD48 revised (2 extra bases on 5' end) x Kt-46.tth
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-46.dra
+>SNORD48 revised (2 extra bases on 5' end) x Kt-46.dra
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-46.eco
+>SNORD48 revised (2 extra bases on 5' end) x Kt-46.eco
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-58.hma
+>SNORD48 revised (2 extra bases on 5' end) x Kt-58.hma
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-U4a.hsa
+>SNORD48 revised (2 extra bases on 5' end) x Kt-U4a.hsa
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-U4b.hsa
+>SNORD48 revised (2 extra bases on 5' end) x Kt-U4b.hsa
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-CD-box.CGU
+>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.CGU
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-CD-box.UGU
+>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.UGU
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-L30e.sce
+>SNORD48 revised (2 extra bases on 5' end) x Kt-L30e.sce
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-SAM-ribo.tte
+>SNORD48 revised (2 extra bases on 5' end) x Kt-SAM-ribo.tte
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-T-box.bsu
+>SNORD48 revised (2 extra bases on 5' end) x Kt-T-box.bsu
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-c-di-GMP-II.cac
+>SNORD48 revised (2 extra bases on 5' end) x Kt-c-di-GMP-II.cac
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised 2 extra bases on 5 end x Kt-G2nA-SAM-riboswitch T. tengcongensi
+>SNORD48 revised (2 extra bases on 5' end) x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
diff -r c690aa928d3d -r 63156f020cd3 test-data/segments_truncated.2.out.txt
--- a/test-data/segments_truncated.2.out.txt	Fri May 06 06:08:36 2016 -0400
+++ b/test-data/segments_truncated.2.out.txt	Thu May 19 04:31:29 2016 -0400
@@ -1,7 +1,7 @@
->CD-box snoRNA x Kt-CD-box.CGU
+>C/D-box snoRNA x Kt-CD-box.CGU
 GCUCUGACCGAAAGGCGUGAUGAGC
 ((((....((.....))....))))	(((((((((....))...)))))))	2.49938964844
->Artificial double CD K-turn construct x Kt-CD-box.UGU
+>Artificial double C/D K-turn construct x Kt-CD-box.UGU
 GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC
 ((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).)))))))))	((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))))))))	-1.26037597656
 ((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).)))))))))	((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))))))))	-1.26037597656
diff -r c690aa928d3d -r 63156f020cd3 test-data/segments_truncated.out.txt
--- a/test-data/segments_truncated.out.txt	Fri May 06 06:08:36 2016 -0400
+++ b/test-data/segments_truncated.out.txt	Thu May 19 04:31:29 2016 -0400
@@ -1,7 +1,7 @@
->CD-box snoRNA x Kt-CD-box.CGU
+>C/D-box snoRNA x Kt-CD-box.CGU
 GCUCUGACCGAAAGGCGUGAUGAGC
 ((((....((.....))....))))	(((((((((....))...)))))))	2.49938964844
->Artificial double CD K-turn construct x Kt-CD-box.UGU
+>Artificial double C/D K-turn construct x Kt-CD-box.UGU
 GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC
 ((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).)))))))))	((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))))))))	-1.26037597656
 ((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).)))))))))	((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))))))))	-1.26037597656
diff -r c690aa928d3d -r 63156f020cd3 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri May 06 06:08:36 2016 -0400
+++ b/tool_dependencies.xml	Thu May 19 04:31:29 2016 -0400
@@ -1,10 +1,16 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="segmentation-fold" version="1.6.3">
-        <repository changeset_revision="97fc2a21b740" name="package_segmentation_fold_1_6_3" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="segmentation-fold" version="1.6.5">
+        <repository changeset_revision="e3ef4c5b6f19" name="package_segmentation_fold_1_6_5" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     
     <package name="python" version="2.7.10">
         <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="fe0870696ca7" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pysam" version="0.8.2.1">
+        <repository changeset_revision="e6c1f548397a" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
 </tool_dependency>
diff -r c690aa928d3d -r 63156f020cd3 utils_filter-by-energy.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils_filter-by-energy.xml	Thu May 19 04:31:29 2016 -0400
@@ -0,0 +1,62 @@
+<tool id="smf_utils_filter-by-energy" name="filter-by-energy" version="@VERSION@-0">
+    <description>Split entries over two files based on the estimated energy</description>
+    
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <requirements>
+        @REQUIREMENTS_UTILS@
+    </requirements>
+    <expand macro="stdio" />
+    
+    <version_command>@VERSION_COMMAND_UTILS@</version_command>
+    
+    <command><![CDATA[
+        segmentation-fold-utils
+            filter-by-energy
+                --energy ${energy}
+                '$dbn_input_file'
+                '$dbn_output_file_larger_or_equal'
+                '$dbn_output_file_smaller'
+    ]]></command>
+
+    <inputs>
+        <param name="dbn_input_file"
+               type="data"
+               format="dbn,txt"
+               label="Input DBN file"
+               help="The 'fasta'-headers should contain the genomic position being used to find overlapping reads in the BAM file"/>
+        <param name="energy"
+               type="float"
+               value="0.0"
+               argument="--energy"
+               label="Energy value"
+               help="Entries with transitions with energy smaller than energy (&lt; e) or without transitions will be put into DBN_OUTPUT_FILE_LARGER_OR_EQUAL and those larger or equal (&gt;= e) to DBN_OUTPUT_FILE_SMALLER" />
+    </inputs>
+
+    <outputs>
+        <data name="dbn_output_file_larger_or_equal"
+              format="dbn"
+              label="${tool.name} on ${dbn_input_file.hid}: ${dbn_input_file.name} - energy larger/equal than selected"/>
+        <data name="dbn_output_file_smaller"
+              format="dbn"
+              label="${tool.name} on ${dbn_input_file.hid}: ${dbn_input_file.name} - energy smaller than selected"/>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="dbn_input_file" value="DBNFile.test_03.in.dbn" ftype="dbn"/>
+            <param name="energy" value='0.0'/>
+
+            <output name="dbn_output_file_larger_or_equal" file="DBNFile.test_03.out.l.dbn" />
+            <output name="dbn_output_file_smaller" file="DBNFile.test_03.out.s.dbn" />
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+Filter based on whether the entries in the DBN file are already annotated or not
+    ]]></help>
+    
+    <expand macro="citations" />
+</tool>