Mercurial > repos > yhoogstrate > segmentation_fold

changeset 6:4d16cf9414cf draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/segmentation_fold commit 3a3c1d069e0a079d8ea7c0b4ac856ef24141b1aa
author erasmus-medical-center
date Fri, 24 Feb 2017 04:18:22 -0500
parents b7cf9b172cfe
children
files macros.xml segmentation-fold.xml test-data/SNORD114-4-revised.scan-for-segments.txt test-data/SNORD118-revised.scan-for-segments.txt test-data/SNORD13-revised.scan-for-segments.txt test-data/SNORD48-revised.scan-for-segments.txt tool_dependencies.xml utils_add-read-counts.xml utils_estimate-energy.xml utils_extract-boxed-sequences.xml utils_filter-annotated-entries.xml utils_filter-by-energy.xml utils_find-boxes.xml utils_fix-fasta-headers.xml
diffstat 14 files changed, 243 insertions(+), 271 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Aug 03 04:54:40 2016 -0400
+++ b/macros.xml	Fri Feb 24 04:18:22 2017 -0500
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">smf-v1.6-5_utils-v2.1.0</token>
+    <token name="@VERSION@">smf-v1.7-0_utils-v2.1.1</token>
 
     <xml name="stdio">
         <stdio>
@@ -8,23 +8,16 @@
         </stdio>
     </xml>
 
-    <token name="@VERSION_COMMAND_SMF@">segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</token>
-    <token name="@VERSION_COMMAND_UTILS@">segmentation-fold-utils --version</token>
-
+    <xml name="version_command">
+        <version_command>echo $(segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')", "$(segmentation-fold-utils --version)</version_command>
+    </xml>
 
-    <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="0.6.1">htseq</requirement>
-        <requirement type="package" version="2.1.0">segmentation-fold-utils</requirement>
-    ]]></token>
-
-    <token name="@REQUIREMENTS_SMF@"><![CDATA[
-        <requirement type="package" version="1.6.5">segmentation-fold</requirement>
-    ]]></token>
-
-
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.7.0">segmentation-fold</requirement><!-- includes utils -->
+        </requirements>
+    </xml>
+    
     <xml name="citations">
         <citations>
             <citation type="bibtex">
--- a/segmentation-fold.xml	Wed Aug 03 04:54:40 2016 -0400
+++ b/segmentation-fold.xml	Fri Feb 24 04:18:22 2017 -0500
@@ -4,34 +4,27 @@
         <import>macros.xml</import>
     </macros>
     
-    <requirements>
-        <requirement type="package" version="1.6.5">segmentation-fold</requirement>
-    </requirements>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
     
-    <expand macro="stdio" />
-    
-    <version_command>@VERSION_COMMAND_SMF@</version_command>
-    
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         segmentation-fold
             
             #if $input.method == "fasta"
-                -f $input.input_fasta
+                -f '${input.input_fasta}'
             #else
-                -s $input.input_sequence
+                -s '${input.input_sequence}'
             #end if
             
             -p $predict_segments
-            -h $min_hairpin_size
+            -H $min_hairpin_size
             
-            #if $parameters.settings == "default"
-                -x "\$SEGMENTATION_FOLD_DEFAULT_XML"
-            #else
-                -x "${parameters.input_xml}"
+            #if $parameters.settings == "custom"
+                -x '${parameters.input_xml}'
             #end if
             
             -t \${GALAXY_SLOTS:-4}
-            > $output_dbn
+            > '${output_dbn}'
     ]]></command>
     
     <inputs>
@@ -41,15 +34,15 @@
                 <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)" />
+                <param name="input_fasta" type="data" format="fasta" label="Fasta file with RNA-sequece" argument="-f" />
             </when>
             <when value="text"> 
-                <param name="input_sequence" type="text" label="RNA-sequece (-s)" />
+                <param name="input_sequence" type="text" label="RNA-sequence" argument="-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)" />
+        <param name="predict_segments" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Enable segment prediction functionality" argument="-p" />
+        <param name="min_hairpin_size" type="integer" min="1" value="3" label="Minimum hairpin size" argument="-h" />
         
         <conditional name="parameters">
             <param name="settings" type="select" label="Energy parameters">
@@ -58,7 +51,7 @@
             </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)" />
+                <param name="input_xml" type="data" format="xml" multiple="false" label="Use custom 'segments.xml'-syntaxed file" argument="-x" />
             </when>
         </conditional>
     </inputs>
@@ -234,7 +227,7 @@
 
 **Authors**
 
-Youri Hoogstrate (yhoogstrate @ github)
+Youri Hoogstrate (GitHub: @yhoogstrate)
     ]]></help>
     
     <expand macro="citations" />
--- a/test-data/SNORD114-4-revised.scan-for-segments.txt	Wed Aug 03 04:54:40 2016 -0400
+++ b/test-data/SNORD114-4-revised.scan-for-segments.txt	Fri Feb 24 04:18:22 2017 -0500
@@ -1,57 +1,74 @@
+>SNORD114-4 revised x Kt-42.dra
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 revised x Kt-42.eco
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 revised x Loop-E-Motif.bac
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 revised x Kt-CD-box.UAU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 revised x Kt-CD-box.UGU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 revised x Kt-CD-box.CAU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 revised x Kt-42.tth
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >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-15.hma
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..)))))	.((((((....(((.((.....((((......))))((....))...)...))))...(((....))).))))))	-6.42471313477
+>SNORD114-4 revised x Kt-U4b.hsa
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 revised x Kt-CD-box.GGU
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 revised x Kt-7 (E. coli)
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 revised x Kt-7 (D. radiodurans)
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-11 (T. thermophilus)
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-11.eco
+>SNORD114-4 revised x Kt-58.hma
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-15.hma
+>SNORD114-4 revised x Kt-46.tth
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
-.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..)))))	.((((((....(((.((.....((((......))))((....))...)...))))...(((....))).))))))	-6.42471313477
->SNORD114-4 revised x Kt-23.tth
+>SNORD114-4 revised x Kt-SAM-ribo.tte
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 revised x Kt-23.eco
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 revised x Kt-38.hma
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-42.hma
+>SNORD114-4 revised x Kt-46.dra
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-42.tth
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-42.dra
+>SNORD114-4 revised x Kt-CD-box.CGU
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-42.eco
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-46.hma
+>SNORD114-4 revised x Kt-T-box.bsu
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-46.tth
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-46.dra
+>SNORD114-4 revised x Kt-23.tth
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 revised x Kt-46.eco
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-58.hma
+>SNORD114-4 revised x Kt-c-di-GMP-II.cac
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 revised x Kt-11 (T. thermophilus)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 revised x Kt-CD-box.AAU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 revised x Kt-L30e.sce
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 revised x Kt-7 (T. thermophilus)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 revised x Kt-42.hma
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
 >SNORD114-4 revised x Kt-U4a.hsa
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-U4b.hsa
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-CD-box.CGU
+>SNORD114-4 revised x Kt-G2nA-SAMribo.bsu
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-CD-box.UGU
+>SNORD114-4 revised x Kt-CD-box.GAU
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-L30e.sce
+>SNORD114-4 revised x Kt-11.eco
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-SAM-ribo.tte
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-T-box.bsu
+>SNORD114-4 revised x Kt-46.hma
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-c-di-GMP-II.cac
+>SNORD114-4 revised x Kt-CD-box.AGU
 CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
->SNORD114-4 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
-CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..)))))	.((((((...(((((.......((((......)))).((((((..........)))))).....)))))))))))	2.00271606445
--- a/test-data/SNORD118-revised.scan-for-segments.txt	Wed Aug 03 04:54:40 2016 -0400
+++ b/test-data/SNORD118-revised.scan-for-segments.txt	Fri Feb 24 04:18:22 2017 -0500
@@ -1,57 +1,75 @@
+>SNORD118 revised x Kt-42.dra
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-42.eco
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Loop-E-Motif.bac
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-CD-box.UAU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-CD-box.UGU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-CD-box.CAU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).)))))	.(((...((((((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).))))))))).	3.36520385742
+>SNORD118 revised x Kt-42.tth
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 revised x Kt-7 G2nA SAM riboswitch (H. marismortui)
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-7 (T. thermophilus)
+>SNORD118 revised x Kt-15.hma
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-U4b.hsa
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-CD-box.GGU
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 revised x Kt-7 (E. coli)
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 revised x Kt-7 (D. radiodurans)
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-11 (T. thermophilus)
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-11.eco
+>SNORD118 revised x Kt-58.hma
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-15.hma
+>SNORD118 revised x Kt-46.tth
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-23.tth
+>SNORD118 revised x Kt-SAM-ribo.tte
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 revised x Kt-23.eco
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 revised x Kt-38.hma
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-42.hma
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-42.tth
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-42.dra
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-42.eco
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-46.hma
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-46.tth
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 revised x Kt-46.dra
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-46.eco
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-58.hma
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-U4a.hsa
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-U4b.hsa
-AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 revised x Kt-CD-box.CGU
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 .(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).)))))	(((((...((((((............))...))))...))......(((((((((...........))))))))).....)))......	-15.038848877
->SNORD118 revised x Kt-CD-box.UGU
+>SNORD118 revised x Kt-T-box.bsu
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-23.tth
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-46.eco
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-c-di-GMP-II.cac
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-11 (T. thermophilus)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-CD-box.AAU
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
 >SNORD118 revised x Kt-L30e.sce
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-SAM-ribo.tte
+>SNORD118 revised x Kt-7 (T. thermophilus)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-42.hma
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-T-box.bsu
+>SNORD118 revised x Kt-U4a.hsa
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-G2nA-SAMribo.bsu
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-c-di-GMP-II.cac
+>SNORD118 revised x Kt-CD-box.GAU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).)))))	(((.(((...(((((......))))))((((.....))))...)).(((((((((...........))))))))).....)))......	-8.30844116211
+>SNORD118 revised x Kt-11.eco
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
->SNORD118 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
+>SNORD118 revised x Kt-46.hma
 AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 revised x Kt-CD-box.AGU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
--- a/test-data/SNORD13-revised.scan-for-segments.txt	Wed Aug 03 04:54:40 2016 -0400
+++ b/test-data/SNORD13-revised.scan-for-segments.txt	Fri Feb 24 04:18:22 2017 -0500
@@ -1,57 +1,74 @@
+>SNORD13 revised x Kt-42.dra
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-42.eco
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Loop-E-Motif.bac
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-CD-box.UAU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-CD-box.UGU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-CD-box.CAU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-42.tth
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 revised x Kt-7 G2nA SAM riboswitch (H. marismortui)
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-7 (T. thermophilus)
+>SNORD13 revised x Kt-15.hma
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-U4b.hsa
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-CD-box.GGU
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 revised x Kt-7 (E. coli)
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 revised x Kt-7 (D. radiodurans)
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-11 (T. thermophilus)
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-11.eco
+>SNORD13 revised x Kt-58.hma
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-15.hma
+>SNORD13 revised x Kt-46.tth
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-23.tth
+>SNORD13 revised x Kt-SAM-ribo.tte
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 revised x Kt-23.eco
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 revised x Kt-38.hma
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-42.hma
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-42.tth
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-42.dra
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-42.eco
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-46.hma
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-46.tth
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 revised x Kt-46.dra
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-46.eco
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-58.hma
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-U4a.hsa
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-U4b.hsa
-GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 revised x Kt-CD-box.CGU
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 (((((.(..((.(((....((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))..))))))	(((((.(.(...((((((.((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))))))))))	3.37054443359
->SNORD13 revised x Kt-CD-box.UGU
+>SNORD13 revised x Kt-T-box.bsu
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-23.tth
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-46.eco
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-c-di-GMP-II.cac
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-11 (T. thermophilus)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-CD-box.AAU
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
 >SNORD13 revised x Kt-L30e.sce
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-SAM-ribo.tte
+>SNORD13 revised x Kt-7 (T. thermophilus)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-42.hma
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-T-box.bsu
+>SNORD13 revised x Kt-U4a.hsa
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-G2nA-SAMribo.bsu
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-c-di-GMP-II.cac
+>SNORD13 revised x Kt-CD-box.GAU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+(((((.(..((.(((....((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))..))))))	(((((((.((((...((((((((((....))))))..)))))...)))))............((((.((((.((........)))))))))).)))))	-9.90228271484
+>SNORD13 revised x Kt-11.eco
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
->SNORD13 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
+>SNORD13 revised x Kt-46.hma
 GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 revised x Kt-CD-box.AGU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
--- a/test-data/SNORD48-revised.scan-for-segments.txt	Wed Aug 03 04:54:40 2016 -0400
+++ b/test-data/SNORD48-revised.scan-for-segments.txt	Fri Feb 24 04:18:22 2017 -0500
@@ -1,56 +1,74 @@
+>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
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 revised (2 extra bases on 5' end) x Loop-E-Motif.bac
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.UAU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.UGU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.CAU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 revised (2 extra bases on 5' end) x Kt-42.tth
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 revised (2 extra bases on 5' end) x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >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-15.hma
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>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.GGU
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >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)
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->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-58.hma
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised (2 extra bases on 5' end) x Kt-15.hma
+>SNORD48 revised (2 extra bases on 5' end) x Kt-46.tth
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised (2 extra bases on 5' end) x Kt-23.tth
+>SNORD48 revised (2 extra bases on 5' end) x Kt-SAM-ribo.tte
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >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
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised (2 extra bases on 5' end) x Kt-42.hma
+>SNORD48 revised (2 extra bases on 5' end) x Kt-46.dra
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->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-CD-box.CGU
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->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-T-box.bsu
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->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-23.tth
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >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-c-di-GMP-II.cac
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 revised (2 extra bases on 5' end) x Kt-11 (T. thermophilus)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.AAU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 revised (2 extra bases on 5' end) x Kt-L30e.sce
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 revised (2 extra bases on 5' end) x Kt-7 (T. thermophilus)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 revised (2 extra bases on 5' end) x Kt-42.hma
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
 >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
-GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.CGU
+>SNORD48 revised (2 extra bases on 5' end) x Kt-G2nA-SAMribo.bsu
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->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-CD-box.GAU
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
->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
+((((((.((.((((((((((.....)))).).).)))).((((...))))...)).))))))....	(((((...(((((((...))).....))))).....(((((............)))))))))....	-10.9268188477
+>SNORD48 revised (2 extra bases on 5' end) x Kt-11.eco
 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-46.hma
 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-CD-box.AGU
 GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+((((((.((.((((((((((.....)))).).).)))).((((...))))...)).))))))....	((...(((((..((..((((.....)))).))((((.((((((...))))..)).)))))))))))	-1.84698486328
--- a/tool_dependencies.xml	Wed Aug 03 04:54:40 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="segmentation-fold" version="1.6.5">
-        <repository changeset_revision="cb5aabdbde26" name="package_segmentation_fold_1_6_5__utils_2_1_0" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    
-
-    <package name="python" version="2.7.10">
-        <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="numpy" version="1.9">
-        <repository changeset_revision="f24fc0b630fc" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="pysam" version="0.8.2.1">
-        <repository changeset_revision="f8fecf1f6eba" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="htseq" version="0.6.1">
-        <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    
-    <package name="segmentation-fold-utils" version="2.1.0">
-        <repository changeset_revision="cb5aabdbde26" name="package_segmentation_fold_1_6_5__utils_2_1_0" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
--- a/utils_add-read-counts.xml	Wed Aug 03 04:54:40 2016 -0400
+++ b/utils_add-read-counts.xml	Fri Feb 24 04:18:22 2017 -0500
@@ -5,18 +5,10 @@
         <import>macros.xml</import>
     </macros>
     
-    <requirements>
-        <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="0.6.1">htseq</requirement>
-        <requirement type="package" version="2.1.0">segmentation-fold-utils</requirement>
-    </requirements>
-    <expand macro="stdio" />
+    <expand macro="requirements" />
+    <expand macro="version_command" />
     
-    <version_command>@VERSION_COMMAND_UTILS@</version_command>
-    
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         ln -f -s '${bam_input_file.metadata.bam_index}' '${bam_input_file}.bai' &&
         
         segmentation-fold-utils
@@ -78,4 +70,4 @@
     ]]></help>
     
     <expand macro="citations" />
-</tool>
\ No newline at end of file
+</tool>
--- a/utils_estimate-energy.xml	Wed Aug 03 04:54:40 2016 -0400
+++ b/utils_estimate-energy.xml	Fri Feb 24 04:18:22 2017 -0500
@@ -5,20 +5,10 @@
         <import>macros.xml</import>
     </macros>
     
-    <requirements>
-        <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="0.6.1">htseq</requirement>
-        <requirement type="package" version="2.1.0">segmentation-fold-utils</requirement>
-
-        <requirement type="package" version="1.6.5">segmentation-fold</requirement>
-    </requirements>
-    <expand macro="stdio" />
+    <expand macro="requirements" />
+    <expand macro="version_command" />
     
-    <version_command>echo $(@VERSION_COMMAND_SMF@)", "$(@VERSION_COMMAND_UTILS@)</version_command>
-    
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         segmentation-fold-utils
             estimate-energy
                 -T \${GALAXY_SLOTS:-2}
@@ -26,7 +16,7 @@
                 #if str($parameters.use_custom_xml) == "true"
                     "${parameters.input_xml}"
                 #else
-                    "\$SEGMENTATION_FOLD_DEFAULT_XML"
+                    "\$(segmentation-fold -X)"
                 #end if
                 
                 -p $precision
@@ -45,7 +35,7 @@
                 type="boolean"
                 truevalue="true"
                 falsevalue="false"
-                selected="false"
+                checked="false"
                 label="Use segment definition from history" />
 
             <when value="false" />
--- a/utils_extract-boxed-sequences.xml	Wed Aug 03 04:54:40 2016 -0400
+++ b/utils_extract-boxed-sequences.xml	Fri Feb 24 04:18:22 2017 -0500
@@ -5,18 +5,10 @@
         <import>macros.xml</import>
     </macros>
     
-    <requirements>
-        <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="0.6.1">htseq</requirement>
-        <requirement type="package" version="2.1.0">segmentation-fold-utils</requirement>
-    </requirements>
-    <expand macro="stdio" />
+    <expand macro="requirements" />
+    <expand macro="version_command" />
     
-    <version_command>@VERSION_COMMAND_UTILS@</version_command>
-    
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         segmentation-fold-utils
             extract-boxed-sequences
 
--- a/utils_filter-annotated-entries.xml	Wed Aug 03 04:54:40 2016 -0400
+++ b/utils_filter-annotated-entries.xml	Fri Feb 24 04:18:22 2017 -0500
@@ -5,18 +5,10 @@
         <import>macros.xml</import>
     </macros>
     
-    <requirements>
-        <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="0.6.1">htseq</requirement>
-        <requirement type="package" version="2.1.0">segmentation-fold-utils</requirement>
-    </requirements>
-    <expand macro="stdio" />
+    <expand macro="requirements" />
+    <expand macro="version_command" />
     
-    <version_command>@VERSION_COMMAND_UTILS@</version_command>
-    
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         segmentation-fold-utils
             filter-annotated-entries
                 --regex '${regex.replace("'","\\'")}'
--- a/utils_filter-by-energy.xml	Wed Aug 03 04:54:40 2016 -0400
+++ b/utils_filter-by-energy.xml	Fri Feb 24 04:18:22 2017 -0500
@@ -5,18 +5,10 @@
         <import>macros.xml</import>
     </macros>
     
-    <requirements>
-        <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="0.6.1">htseq</requirement>
-        <requirement type="package" version="2.1.0">segmentation-fold-utils</requirement>
-    </requirements>
-    <expand macro="stdio" />
+    <expand macro="requirements" />
+    <expand macro="version_command" />
     
-    <version_command>@VERSION_COMMAND_UTILS@</version_command>
-    
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         segmentation-fold-utils
             filter-by-energy
                 --energy ${energy}
--- a/utils_find-boxes.xml	Wed Aug 03 04:54:40 2016 -0400
+++ b/utils_find-boxes.xml	Fri Feb 24 04:18:22 2017 -0500
@@ -5,19 +5,10 @@
         <import>macros.xml</import>
     </macros>
     
-    <requirements>
-        <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="0.6.1">htseq</requirement>
-        <requirement type="package" version="2.1.0">segmentation-fold-utils</requirement>
-    </requirements>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
     
-    <expand macro="stdio" />
-
-    <version_command>@VERSION_COMMAND_UTILS@</version_command>
-    
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         segmentation-fold-utils
             find-boxes
                 --box1 '${box1}'
@@ -72,7 +63,7 @@
 
     <tests>
         <test>
-            <param name="fasta_input" value="FindBoxes.genome.fa" format="fasta" />
+            <param name="fasta_input" value="FindBoxes.genome.fa" ftype="fasta" />
             <param name="box1" value="NRUGAUG" />
             <param name="box2" value="CUGA" />
             <param name="forward" value="--forward" />
--- a/utils_fix-fasta-headers.xml	Wed Aug 03 04:54:40 2016 -0400
+++ b/utils_fix-fasta-headers.xml	Fri Feb 24 04:18:22 2017 -0500
@@ -5,19 +5,10 @@
         <import>macros.xml</import>
     </macros>
     
-    <requirements>
-        <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="0.6.1">htseq</requirement>
-        <requirement type="package" version="2.1.0">segmentation-fold-utils</requirement>
-    </requirements>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
     
-    <expand macro="stdio" />
-
-    <version_command>@VERSION_COMMAND_UTILS@</version_command>
-    
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         segmentation-fold-utils
             fix-fasta-headers
                 '${fasta_input}'
@@ -28,8 +19,8 @@
         <param name="fasta_input"
                type="data"
                format="fasta"
-               argument="-f"
-               label="Fasta file with RNA-sequece" />
+               label="Fasta file with RNA-sequece"
+               argument="-f" />
     </inputs>
 
     <outputs>
@@ -40,12 +31,12 @@
 
     <tests>
         <test>
-            <param name="fasta_input" value="test_22.fa" format="fasta" />
+            <param name="fasta_input" value="test_22.fa" ftype="fasta" />
             
             <output name="fasta_output" file="test_22.fixed.fa" />
         </test>
         <test>
-            <param name="fasta_input" value="test_23.fa" format="fasta" />
+            <param name="fasta_input" value="test_23.fa" ftype="fasta" />
             
             <output name="fasta_output" file="test_23.fixed.fa" />
         </test>