# HG changeset patch
# User bgruening
# Date 1670250529 0
# Node ID 7554c0df9139bb9e0d85c8683494aa5975191824
# Parent  94b0468f0db80bae3862e1f4449a87d8db4cfc85
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042

diff -r 94b0468f0db8 -r 7554c0df9139 locarna.tar.bz2
Binary file locarna.tar.bz2 has changed
diff -r 94b0468f0db8 -r 7554c0df9139 locarna_multiple.xml
--- a/locarna_multiple.xml	Sat Jan 21 17:38:28 2017 -0500
+++ b/locarna_multiple.xml	Mon Dec 05 14:28:49 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="locarna_multiple" name="LocARNA Multiple Aligner" version="@VERSION@.1">
+<tool id="locarna_multiple" name="LocARNA Multiple Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>
         Multiple Alignment and Folding of RNAs (mlocarna)
     </description>
@@ -22,7 +22,8 @@
     #end if
 
     --tgtdir mlocarna_results
-    --width 60
+    ## maybe reenable later? see  https://github.com/s-will/LocARNA/issues/77
+    ## --width 60
     
     ## -------------------- alignment mode and specific options
     #
@@ -65,10 +66,9 @@
 
     @STDOUT_ARGS@
 
-    #if 'clustal_strict' in str($outputs).split(",")
+    #if 'strict' in str($outputs).split(",")
         && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln
     #end if
-
     ]]></command>
 
     <inputs>
@@ -93,8 +93,7 @@
                    help="Note that local alignment mode usually requires to turn off 
                          the 'max-diff' heuristic (maximal difference for alignment traces)."
                    >
-                <option value="global_locarna">Global alignment
-                (LocARNA)</option>
+                <option value="global_locarna">Global alignment (LocARNA)</option>
                 <option value="local_locarna">Local alignment (LocARNA)</option>
                 <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option>
                 <option value="sparse">Global fast alignment (SPARSE)</option>
@@ -129,46 +128,33 @@
                     <expand macro="common_heuristic_parameters_sparse" />
                 </section>
             </when>
-
         </conditional>
-        
-        <param name="outputs" type="select" display="checkboxes" multiple="True" 
+        <param name="outputs" type="select" display="checkboxes" multiple="true" 
                label="Output options">
-            <option value="clustal_strict" selected="True">Output alignment
-            in ClustalW format</option>
-            <option value="clustal" selected="False">Output alignment
-            in constraint-annotated ClustalW format</option>
-            <option value="stockholm" selected="False">Output
-            alignment in Stockholm format</option>
-            <option value="pp" selected="False">Output
-            alignment in LocARNA's PP 2.0 format</option>
-            <option value="mlocarna_results" selected="False">
-            Output LocARNA results archive (tar.gz)</option>
+            <option value="strict" selected="true">Alignment in ClustalW format</option>
+            <option value="clustal" selected="false">Alignment in constraint-annotated ClustalW format</option>
+            <option value="stockholm" selected="false">Alignment in Stockholm format</option>
+            <option value="pp" selected="false">Alignment in LocARNA's PP 2.0 format</option>
+            <option value="mlocarna_results" selected="false">LocARNA results archive (tar.gz)</option>
         </param>
-        
         <param name="stdout_verbosity" type="select" label="Standard output verbosity">
-            <option value="--quiet">Don't report standard
-            output</option>
+            <option value="--quiet">Don't report standard output</option>
             <option value="">Non verbose</option>
             <option value="--verbose">Verbose</option>
             <option value="--moreverbose">More verbose</option>
         </param>
-               
         <section name="Scoring" title="Scoring parameters">
             <expand macro="common_scoring_parameters" />
         </section>
-        
         <section name="Folding" title="RNA folding parameters">
             <expand macro="plfolding_parameters" />
             <expand macro="common_folding_parameters" />
             <expand macro="alifold_consensus_parameter" />
         </section>
-
         <section name="Heuristics" title="Heuristic parameters">
             <expand macro="common_heuristic_parameters" />
             <expand macro="max_diff_parameters_aln" />
         </section>
-
         <section name="Constraints" title="Constraint parameters">
             <expand macro="bed_anchors" />
             <expand macro="common_constraint_parameters" />
@@ -180,33 +166,59 @@
     </outputs>
     
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input_data" value="archaea.fa" />
             <param name="stdout_verbosity" value="" />
             <param name="max_diff_mode_selector" value="max-diff" />
             <param name="max_diff" value="20" />
-            <output name="stdout" file="archaea-default.stdout" />
+            <param name="outputs" value="clustal,strict"/>
+            <output name="stdout" file="archaea-default.stdout" lines_diff="2" />
+            <output name="clustal">
+                <assert_contents>
+                    <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
+            <output name="clustal_strict">
+                <assert_contents>
+                    <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_data" value="haca.snoRNA.fa" />
             <param name="stdout_verbosity" value="" />
-            <output name="stdout" file="haca.snoRNA-default.stdout" />
+            <output name="stdout" file="haca.snoRNA-default.stdout" lines_diff="2" />
+            <output name="clustal_strict">
+                <assert_contents>
+                    <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_data" value="archaea.fa" />
             <param name="stdout_verbosity" value="" />
             <param name="outputs" value="clustal" />
             <param name="alignment_mode_selector" value="probabilistic" />
-            <output name="clustal" file="archaea-probabilistic.aln" />
+            <output name="stdout">
+                <assert_contents>
+                    <has_text text="mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
+            <output name="clustal" file="archaea-probabilistic.aln" lines_diff="2"/>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_data" value="archaea.fa" />
             <param name="stdout_verbosity" value="" />
             <param name="outputs" value="clustal" />
             <param name="max_diff_mode_selector" value="max-diff-aln" />
             <param name="max_diff_aln" value="archaea-ref.aln" />
             <param name="max_diff" value="2" />
-            <output name="clustal" file="archaea-ref_result.aln" />
+            <output name="stdout">
+                <assert_contents>
+                    <has_text text="mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
+            <output name="clustal" file="archaea-ref_result.aln" lines_diff="2"/>
         </test>
     </tests>
 
diff -r 94b0468f0db8 -r 7554c0df9139 macros.xml
--- a/macros.xml	Sat Jan 21 17:38:28 2017 -0500
+++ b/macros.xml	Mon Dec 05 14:28:49 2022 +0000
@@ -1,9 +1,12 @@
 <macros>
-    <token name="@VERSION@">1.9.0</token>
+    <token name="@TOOL_VERSION@">1.9.2.3</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">21.09</token>
 
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">locarna</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">locarna</requirement>
+            <requirement type="package" version="4.2.2">r-base</requirement>  
         </requirements>
     </xml>
 
@@ -46,15 +49,15 @@
     </xml>
     
     <xml name="common_scoring_parameters">
-        <param name="struct_weight" argument="struct-weight"
+        <param argument="--struct-weight"
                label="Structure weight" type="integer" 
                value="200" min="0" max="800" />
-        <param name="indel_opening" argument="indel-opening"
+        <param argument="--indel-opening"
                label="Indel opening score" type="integer"
                value="-500" max="0" min="-1500" />
-        <param argument="indel" label="Indel score" type="integer" 
+        <param argument="--indel" label="Indel score" type="integer" 
                value="-350" min="-1000" max="0" />
-        <param argument="tau" type="integer" value="50"
+        <param argument="--tau" type="integer" value="50"
                min="0" max="200"
                label="Sequence contribution at structure match in percent"/> 
 
@@ -78,17 +81,17 @@
     </xml>
 
     <xml name="plfolding_parameters">
-        <param name="plfold_span" argument="--plfold-span" 
+        <param argument="--plfold-span" 
                type="integer" value="150" min="-1" max="400" 
                label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />
         
-        <param name="plfold_winsize" argument="--plfold-winsize"
+        <param argument="--plfold-winsize"
                type="integer" value="300"  min="-1" max="800" 
                label="Window size for local folding" />
     </xml>
     
     <xml name="common_folding_parameters">
-        <param name="rnafold_temperature" argument="rnafold-temperature"
+        <param argument="rnafold-temperature"
                type="float" value="37.0" min="10" max="50"
                label="Temperature for RNAfold (RNAfold's -T option)" />
     </xml>
@@ -147,16 +150,18 @@
 
     </token>
 
-    <token name="@CONSTRAINT_ARGS@">
-        ## -------------------- constraint parameters
-        $Constraints.lonely_pairs
-
+    <token name="@CONSTRAINT_ARGS_WOLP@">
         #if $Constraints.maxBPspan != -1
             --maxBPspan $Constraints.maxBPspan
         #end if
 
         $Constraints.ignore_constraints
     </token>
+    <token name="@CONSTRAINT_ARGS@">
+        ## -------------------- constraint parameters
+        $Constraints.lonely_pairs
+        @CONSTRAINT_ARGS_WOLP@
+    </token>
 
     <token name="@STDOUT_ARGS@">
         $stdout_verbosity
@@ -171,7 +176,7 @@
                label="Restrict alignable positions by maximum difference" 
                help="(max-diff*)">
             <option value="off">Off</option>
-            <option value="max-diff" selected="True">Maximal difference of aligned positions</option>
+            <option value="max-diff" selected="true">Maximal difference of aligned positions</option>
             <option value="max-diff-at-am">Maximal difference of aligned positions at arc matches</option> 
             <yield />
         </param>
@@ -180,12 +185,12 @@
     <xml name="max_diff_parameters_standard_cases">
         <when value="off" />
         <when value="max-diff">
-            <param  name="max_diff" argument="max-diff" type="integer"
+            <param argument="--max-diff" type="integer"
                     value="60" min="-1" max="300"
                     label="Maximal difference of aligned positions" />
         </when>
         <when value="max-diff-at-am">
-            <param  name="max_diff_at_am" argument="max-diff-at-am" type="integer" 
+            <param argument="--max-diff-at-am" type="integer" 
                     value="60" min="-1" max="300"
                     label="Maximal difference of aligned positions,
                            only at arc match positions" />
@@ -206,13 +211,13 @@
             </expand>
             <expand macro="max_diff_parameters_standard_cases" />
             <when value="max-diff-aln">
-                <param name="max_diff_aln" argument="max-diff-aln" type="data" format="clustal"
+                <param argument="--max-diff-aln" type="data" format="clustal"
                        label="Reference alignment"
                        />
-                <param  name="max_diff" argument="max-diff" type="integer"
+                <param argument="--max-diff" type="integer"
                         value="60" min="-1" max="300"
                         label="Maximal difference of aligned positions" />
-                <param name="max_diff_relax" argument="max-diff-relax" type="boolean"
+                <param argument="--max-diff-relax" type="boolean"
                        truevalue="--max-diff-relax" falsevalue=""
                        checked="False"
                        label="Relax deviation constraints in multiple
@@ -223,75 +228,79 @@
     </xml>
 
     <xml name="common_heuristic_parameters">
-        <param  name="min_prob" argument="min-prob" type="float" value="0.0005" 
+        <param argument="--min-prob" type="float" value="0.0005" 
                 min="0.0" max="0.2"
                 label="Minimal / cutoff probability" /> 
     
-        <param  name="max_diff_am" argument="max-diff-am" 
+        <param argument="--max-diff-am" 
                 type="integer" value="30" 
                 min="-1" max="300"
                 label="Maximal difference for sizes of matched arcs (-1=off)" />
         
-        <param  name="max_bps_length_ratio" argument="max-bps-length-ratio"
+        <param  argument="--max-bps-length-ratio"
                 type="float" value="0.0" min="0.0" max="10.0" 
                 label="Maximal ratio 'number of considered base pairs' by
                        'sequence length' (default: 0.0 = no effect)" />
     </xml>
     
     <xml name="common_heuristic_parameters_sparse">
-        <param  name="prob_unpaired_in_loop_threshold" argument="prob-unpaired-in-loop-threshold" type="float" value="0.00005" 
+        <param argument="--prob-unpaired-in-loop-threshold" type="float" value="0.00005" 
                 min="0.0" max="0.2"
                 label="Probability threshold for unpaired bases in loops" /> 
 
-        <param  name="prob_basepair_in_loop_threshold" argument="prob-basepair-in-loop-threshold" type="float" value="0.0001" 
+        <param argument="--prob-basepair-in-loop-threshold" type="float" value="0.0001" 
                 min="0.0" max="0.2"
                 label="Probability threshold for base pairs in loops" />       
     </xml>
     
     <xml name="in_loop_ratio_parameters">
-        <param  name="max_uil_length_ratio" argument="max-uil-length-ratio"
+        <param argument="--max-uil-length-ratio"
                 type="float" value="0.0" min="0.0" max="10.0" 
                 label="Maximal ratio 'number considered unpaired bases in loops' by
                        'sequence length' (default: 0.0; no effect)" />
         
-        <param  name="max_bpil_length_ratio" argument="max-bpil-length-ratio"
+        <param argument="--max-bpil-length-ratio"
                 type="float" value="0.0" min="0.0" max="10.0" 
                 label="Maximal ratio 'number of considered base pairs in loops'
                        by 'sequence length' (default: 0.0; no effect)" />
     </xml>
 
     <xml name="exparnap_in_loop_parameters">
-        <param  name="prob_unpaired_in_loop_threshold"
-                argument="prob_unpaired_in_loop_threshold"
+        <param argument="--prob_unpaired_in_loop_threshold"
                 type="float" value="0.01" min="0.0" max="1.0" 
                 label="Probability threshold for unpaired bases in loops" />
-        <param  name="prob_basepair_in_loop_threshold"
-                argument="prob_basepair_in_loop_threshold"
+        <param argument="--prob_basepair_in_loop_threshold"
                 type="float" value="0.01" min="0.0" max="1.0" 
                 label="Probability threshold for base pairs in loops" />
     </xml>
 
     <xml name="alifold_consensus_parameter">
-        <param  name="alifold_consensus_dp" argument="alifold-consensus-dp" 
+        <param argument="--alifold-consensus-dp" 
                 type="boolean" checked="False" 
                 truevalue="--alifold-consensus-dp" falsevalue=""
                 label="Compute consensus dot plot by alifold" />
     </xml>
     
-    <xml name="common_constraint_parameters">
-        <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" 
-               checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" />
-        <param name="maxBPspan" argument="--maxBPspan" 
+    <xml name="common_constraint_parameters_woLP">
+        <yield/>
+        <param argument="--maxBPspan" 
                type="integer" value="-1" min="-1" max="400" 
                label="Maximum basepair span by RNAfold; -1 for arbitrary span" />
-        <param name="ignore_constraints" argument="ignore-constraints"
+        <param argument="--ignore-constraints"
                type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue=""
                help="Ignore all anchor and structure constraints given
                      in the fasta(-ish) input." />
     </xml>
 
+    <xml name="common_constraint_parameters">
+        <expand macro="common_constraint_parameters_woLP">
+            <param argument="--noLP" name="lonely_pairs" type="boolean" truevalue="" falsevalue="--noLP" 
+                   checked="true" label="Allow lonely base-pairs"/>
+        </expand>
+    </xml>
+
     <xml name="standard_outupt">
-        <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
+        <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout">
             <filter>stdout_verbosity != '--quiet'</filter>
         </data>
     </xml>
@@ -299,25 +308,25 @@
     <xml name="mlocarna_outputs">
         <expand macro="standard_outupt" />
         <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln"
-              label="${tool.name} alignment (annotated clustal) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (annotated clustal)">
             <filter>'clustal' in outputs</filter>
         </data>
         <data format="clustal" name="clustal_strict" 
               from_work_dir="mlocarna_results/results/result.strict-aln"
-              label="${tool.name} alignment (clustal) on ${on_string}">
-            <filter>'clustal_strict' in outputs</filter>
+              label="${tool.name} on ${on_string}: alignment (clustal)">
+            <filter>'strict' in outputs</filter>
         </data>
         <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk"
-              label="${tool.name} alignment (stockholm) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (stockholm)">
             <filter>'stockholm' in outputs</filter>
         </data>
         <data format="txt" name="pp"
               from_work_dir="mlocarna_results/results/result.pp"
-              label="${tool.name} alignment (PP 2.0) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (PP 2.0)">
             <filter>'pp' in outputs</filter>
         </data>
         <data format="tar.gz" name="mlocarna_results_tgz"
-              label="${tool.name} results archive on ${on_string}">
+              label="${tool.name} on ${on_string}: results archive">
             <filter>'mlocarna_results' in outputs</filter>
         </data>
     </xml>
@@ -330,8 +339,5 @@
             <citation type="doi">10.1186/s12859-014-0404-0</citation>
         </citations>
     </xml>
-
-
-
 </macros>
 
diff -r 94b0468f0db8 -r 7554c0df9139 test-data/archaea-default.stdout
--- a/test-data/archaea-default.stdout	Sat Jan 21 17:38:28 2017 -0500
+++ b/test-data/archaea-default.stdout	Mon Dec 05 14:28:49 2022 +0000
@@ -6,13 +6,4 @@
 Perform progressive alignment ...
 
 
-
-vhuU               AG-CUCACAACCGAACCC-AU------------UUGGGAGGUUGUGAGCU-
-fwdB               AU-GUUGGAGGGGAACCC-GU------------AAGGGACCCUCCAAGAU-
-selD               UUACGAUGUGCCGAACCCUUU------------AAGGGAGGCACAUCGAAA
-hdrA               GG--CACCACUCGAAGGC--U------------AAGCCAAAGUGGUG-CU-
-vhuD               GU--UCUCUCGGGAACCCGUC------------AAGGGACCGAGAGA-AC-
-fruA               ---CCUCGAGGGGAACCC-GA------------AAGGGACCCGAGAGG---
-fdhA               CG-CCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGGCG-
-
-alifold            ((.(((((((((...(((.................))).))))))))))). (-31.59 = -20.01 + -11.58)
+alifold            ((.(((((((((...(((.................))).))))))))))). (-31.36 = -20.01 + -11.34)
diff -r 94b0468f0db8 -r 7554c0df9139 test-data/archaea_relplot.scr
--- a/test-data/archaea_relplot.scr	Sat Jan 21 17:38:28 2017 -0500
+++ b/test-data/archaea_relplot.scr	Mon Dec 05 14:28:49 2022 +0000
@@ -48,7 +48,7 @@
 par(mar=c(6,2.5,1,1))
 
 # open plot (and draw threshold)
-plot(c(0),c(0),type="l",                                        
+plot(c(0),c(0),type="l",
      xlab="",ylab="",
      xlim=the_xlim,ylim=c(0,maxy),
      yaxp=c(0,1,2))
@@ -87,15 +87,15 @@
 colors<-c(colors,colors);
 
 if (0>0) {
-  
+
   for (i in 1:0) {
     orientation <- signals[signal_starts[i]+signal_sizes[i]*2];
     sig_y  <- maxy-i*anno_space;
-    
+
     for (j in 0:(signal_sizes[i]-1)) {
 
       sig_x <- c(signals[signal_starts[i]+j*2],signals[signal_starts[i]+j*2+1]);
-          
+
       ## draw arrows
       if (orientation!=0) {
         the_code <- 1+(orientation+1)/2;
@@ -109,9 +109,9 @@
 
 #draw inferred on-signal
 hit_color <- rgb(0.1,0.6,0.1,0.9)
-  
+
 if (0!=1) {
-  
+
   on  <- c(0,4,33,44,49);
   off <- c(3,20,43,48,51);
 
diff -r 94b0468f0db8 -r 7554c0df9139 test-data/haca.snoRNA-c.aln
--- a/test-data/haca.snoRNA-c.aln	Sat Jan 21 17:38:28 2017 -0500
+++ b/test-data/haca.snoRNA-c.aln	Mon Dec 05 14:28:49 2022 +0000
@@ -1,22 +1,15 @@
-CLUSTAL W --- LocARNA 1.9.0
-
-ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGG
-ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU
-ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGC
-ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCU
-#A1                ............................................................
-#A2                ............................................................
+CLUSTAL W --- LocARNA 1.9.2.3
 
-ACA7               AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
-ACA30              GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
-ACA5               UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
-ACA59              GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
-#A1                ....AAAAAA..................................................
-#A2                ....123456..................................................
+ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG
+ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGCUGCCACAGAAACAC--UGUGACUCAUGG------GCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGC-UGGCCCAUG--GGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+#A1                ................................................................AAAAAA..................................................
+#A2                ................................................................123456..................................................
 
-ACA7               AUUGGA--AGA---CACU-CUGCG-----ACA
-ACA30              CAACUG--UCA---CUCA-AUGGG-----ACA
-ACA5               GGAUAA--AUU---UGGU-UACAG-----ACA
+ACA7               AUUGGAA-----GACACUC-UGC-----GACA
+ACA30              CAACUGU-----CACUCAA-UGG-----GACA
+ACA5               GGAUAAA-----UUUGGUU-ACA-----GACA
 ACA59              ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
 #A1                .............................BBB
 #A2                .............................123
diff -r 94b0468f0db8 -r 7554c0df9139 test-data/haca.snoRNA-default.stdout
--- a/test-data/haca.snoRNA-default.stdout	Sat Jan 21 17:38:28 2017 -0500
+++ b/test-data/haca.snoRNA-default.stdout	Mon Dec 05 14:28:49 2022 +0000
@@ -6,28 +6,5 @@
 Perform progressive alignment ...
 
 
-
-ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUUCGGAA-AGGG
-ACA30              UGGCACUUUCACAG--UUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU
-ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAA--GGC
-ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUGGGUGAC--CCU
-#A1                ............................................................
-#A2                ............................................................
-
-ACA7               AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
-ACA30              GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
-ACA5               UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
-ACA59              GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
-#A1                ....AAAAAA..................................................
-#A2                ....123456..................................................
-
-ACA7               AUUGGA--AGA---CACU-CUGCG-----ACA
-ACA30              CAACUG--UCA---CUCA-AUGGG-----ACA
-ACA5               GGAUAA--AUU---UGGU-UACAG-----ACA
-ACA59              ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
-#A1                .............................BBB
-#A2                .............................123
-
-alifold            .((((((((........((((.(((((((......))))))).))))......))..)))
-                   ))).............((((((.....((.....((((((((((((.....)))))))))
-                   )))......)).....)).))))......... (-61.69 = -33.85 + -27.84)
+alifold            .((((((((........((((.(((((((......))))))).))))......))..)))))).............(((((((...((......((((((((((((.....)))))))))
+                   ))).........)).))).))))......... (-62.29 = -34.50 + -27.79)
diff -r 94b0468f0db8 -r 7554c0df9139 test-data/haca.snoRNA.aln
--- a/test-data/haca.snoRNA.aln	Sat Jan 21 17:38:28 2017 -0500
+++ b/test-data/haca.snoRNA.aln	Mon Dec 05 14:28:49 2022 +0000
@@ -1,16 +1,11 @@
-CLUSTAL W --- LocARNA 1.9.0
-
-ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGG
-ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU
-ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGC
-ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCU
+CLUSTAL W --- LocARNA 1.9.2.3
 
-ACA7               AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
-ACA30              GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
-ACA5               UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
-ACA59              GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG
+ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGCUGCCACAGAAACAC--UGUGACUCAUGG------GCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGC-UGGCCCAUG--GGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
 
-ACA7               AUUGGA--AGA---CACU-CUGCG-----ACA
-ACA30              CAACUG--UCA---CUCA-AUGGG-----ACA
-ACA5               GGAUAA--AUU---UGGU-UACAG-----ACA
+ACA7               AUUGGAA-----GACACUC-UGC-----GACA
+ACA30              CAACUGU-----CACUCAA-UGG-----GACA
+ACA5               GGAUAAA-----UUUGGUU-ACA-----GACA
 ACA59              ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
diff -r 94b0468f0db8 -r 7554c0df9139 test-data/tRNA_2.aln
--- a/test-data/tRNA_2.aln	Sat Jan 21 17:38:28 2017 -0500
+++ b/test-data/tRNA_2.aln	Mon Dec 05 14:28:49 2022 +0000
@@ -1,7 +1,4 @@
-CLUSTAL W --- LocARNA 1.9.0 --- Score: 2875
+CLUSTAL W --- LocARNA 1.9.2.3 --- Score: 2587
 
-D10744             GGAAAAUU-GAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGG
-AF008220           GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGG-----------UCG
-
-D10744             UGAGUUCGAAUCUCACAUUUUCCG
-AF008220           GCGGUUCGAGCCCGUCAUCCUCCA
+D10744             GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
+AF008220           GGAGGAUUAGC--UCAGCUGGGAGAGCAUCUGCCUUA-------CAAGCAGAGGGUCGGCG-GUUCGAGCCCGUCAUCCUCCA
diff -r 94b0468f0db8 -r 7554c0df9139 test-data/tRNA_2.epms
--- a/test-data/tRNA_2.epms	Sat Jan 21 17:38:28 2017 -0500
+++ b/test-data/tRNA_2.epms	Mon Dec 05 14:28:49 2022 +0000
@@ -1,4 +1,4 @@
 epm_id	 score	 structure	 positions
-0	3583	((()))	1:4 2:5 3:6 80:67 81:68 82:69 
+0	3587	((()))	1:4 2:5 3:6 80:67 81:68 82:69 
 1	3593	((()))	1:1 2:2 3:3 80:70 81:71 82:72