changeset 2:e66514da3a99 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042
author bgruening
date Mon, 05 Dec 2022 13:58:16 +0000
parents 8723e3f8e422
children a80f279b4ad0
files locarna.tar.bz2 locarna_exparnap.xml macros.xml test-data/archaea-default.stdout test-data/archaea_relplot.scr test-data/haca.snoRNA-c.aln test-data/haca.snoRNA-default.stdout test-data/haca.snoRNA.aln test-data/tRNA_2.aln test-data/tRNA_2.epms
diffstat 10 files changed, 124 insertions(+), 157 deletions(-) [+]
line wrap: on
line diff
Binary file locarna.tar.bz2 has changed
--- a/locarna_exparnap.xml	Sat Jan 21 17:38:46 2017 -0500
+++ b/locarna_exparnap.xml	Mon Dec 05 13:58:16 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="locarna_exparnap" name="LocARNA Exact Matcher" version="@VERSION@.0">
+<tool id="locarna_exparnap" name="LocARNA Exact Matcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>
         Pairwise Simultaneous Matching and Folding of RNAs (ExpaRNA-P)
     </description>
@@ -28,11 +28,13 @@
     --struct-mismatch-score $Scoring.struct_mismatch_score
 
     @HEURISTIC_ARGS@
+    --max-uil-length-ratio $Heuristics.max_uil_length_ratio
+    --max-bpil-length-ratio $Heuristics.max_bpil_length_ratio
     --prob_unpaired_in_loop_threshold $Heuristics.prob_unpaired_in_loop_threshold
     --prob_basepair_in_loop_threshold $Heuristics.prob_basepair_in_loop_threshold
 
     @CONSTRAINT_ARGS@
-
+    @FOLDING_ARGS@
     ## -------------------- other parameters
     #
     #if str($Other.subopt.subopt_selector) == "on"
@@ -94,47 +96,47 @@
                help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
                />
 
-        <param name="outputs" type="select" display="checkboxes" multiple="True"
+        <param name="outputs" type="select" display="checkboxes" multiple="true"
                label="Output options">
-            <option value="postscript" selected="False">Best EPM chain
+            <option value="postscript" selected="false">Best EPM chain
             as colored postscript</option>
-            <option value="anchors-fasta" selected="False">Fasta with anchor
+            <option value="anchors-fasta" selected="false">Fasta with anchor
             constraints from chaining</option>
-            <option value="anchors-pp" selected="False">LocARNA PP
+            <option value="anchors-pp" selected="false">LocARNA PP
             files merging input PPs and anchor constraints from
             chaining</option>
-            <option value="clustal" selected="False">Chain as
+            <option value="clustal" selected="false">Chain as
             alignment in Clustal format</option>
-            <option value="epm_list" selected="False">List of the found EPMs</option>
-            <option value="chained_epm_list" selected="False">List of
+            <option value="epm_list" selected="false">List of the found EPMs</option>
+            <option value="chained_epm_list" selected="false">List of
             EPMs in the best chain</option>
         </param>
 
         <param name="stdout_verbosity" type="select" label="Standard output verbosity">
             <option value="--quiet">Don't report standard
             output</option>
-            <option value="" selected="True">Non verbose</option>
+            <option value="" selected="true">Non verbose</option>
             <option value="--verbose">Verbose</option>
         </param>
 
         <section name="Scoring" title="Scoring parameters">
-            <param argument="alpha_1"
+            <param argument="--alpha_1"
                    type="integer" value="1" min="0" max="50"
                    label="Sequence score factor"
                    />
-            <param argument="alpha_2"
+            <param argument="--alpha_2"
                    type="integer" value="5" min="0" max="50"
                    label="Structure score factor"
                    />
-            <param name="no_stacking" argument="no-stacking" type="boolean"
+            <param argument="--no-stacking" type="boolean"
                    truevalue="" falsevalue="--no-stacking"
                    label="Add stacking terms"
                    />
-            <param argument="alpha_3"
+            <param argument="--alpha_3"
                    type="integer" value="5" min="0" max="50"
                    label="Stacking score factor"
                    />
-            <param name="struct_mismatch_score" argument="struct-mismatch-score"
+            <param argument="--struct-mismatch-score"
                    type="integer" value="-10" min="-100" max="0"
                    label="Score for nucleotide mismatch in base pair match"
                    />
@@ -167,33 +169,33 @@
                 </param>
                 <when value="off" />
                 <when value="on">
-                    <param name="diff_to_opt_score" argument="diff-to-opt-score"
+                    <param argument="--diff-to-opt-score"
                            type="integer" value="-1" min="-20" max="0"
                            label="Maximum score difference to optimum" />
-                    <param name="number_of_EPMs" argument="number-of-EPMs"
+                    <param argument="--number-of-EPMs"
                            type="integer" value="100" min="1" max="10000"
                            label="Maximal number of EPMs" />
                 </when>
             </conditional>
 
-            <param name="min_score" argument="min-score"
+            <param argument="--min-score"
                    type="integer" value="30" min="0" max="1000"
                    label="Minimum score of EPM" />
 
-            <param name="inexact_struct_match" argument="inexact-struct-match" type="boolean"
+            <param argument="--inexact-struct-match" type="boolean"
                    truevalue="--inexact-struct-match" falsevalue=""
                    label="Allow inexact structure matches"/>
 
-            <param name="add_filter" argument="add-filter" type="boolean"
-                   truevalue="--add-filter" falsevalue="" checked="False"
+            <param argument="--add-filter" type="boolean"
+                   truevalue="--add-filter" falsevalue="" checked="false"
                    label="Apply an additional filter to enumerate only
                           EPMs that are maximally extended (only inexact)"/>
 
-            <param name="no_chaining" argument="no-chaining" type="boolean"
-                   truevalue="" falsevalue="--no-chaining" checked="True"
+            <param argument="--no-chaining" type="boolean"
+                   truevalue="" falsevalue="--no-chaining" checked="true"
                    label="Find best overall chain by chaining"/>
 
-            <param name="out_min_prob" argument="out-min-prob"
+            <param argument="--out-min-prob"
                    type="float" value="0.0005" min="0" max="1"
                    label="Minimal probability in output (min-prob overrides if smaller)"/>
 
@@ -203,45 +205,51 @@
     <outputs>
         <expand macro="standard_outupt" />
         <data format="ps" name="ps_fileA"
-              label="${tool.name} chain in RNA 1 (postscript) on ${on_string}">
+              label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">
             <filter>'postscript' in outputs</filter>
         </data>
         <data format="ps" name="ps_fileB"
-              label="${tool.name} chain in RNA 2 (postscript) on ${on_string}">
+              label="${tool.name} on ${on_string}: chain in RNA 2 (postscript)">
             <filter>'postscript' in outputs</filter>
         </data>
         <data format="txt" name="anchors_fasta"
-              label="${tool.name} anchor constraints from chain (fasta) on ${on_string}">
+              label="${tool.name} on ${on_string}: anchor constraints from chain (fasta)">
             <filter>'anchors-fasta' in outputs</filter>
         </data>
         <data format="txt" name="anchors_ppA"
-              label="${tool.name} anchors for RNA 1 (pp) on ${on_string}">
+              label="${tool.name} on ${on_string}: anchors for RNA 1 (pp)">
             <filter>'anchors-pp' in outputs</filter>
         </data>
         <data format="txt" name="anchors_ppB"
-              label="${tool.name} anchors for RNA 2 (pp) on ${on_string}">
+              label="${tool.name} on ${on_string}: anchors for RNA 2 (pp)">
             <filter>'anchors-pp' in outputs</filter>
         </data>
         <data format="clustal" name="clustal"
-              label="${tool.name} chain as alignment (clustal) on ${on_string}">
+              label="${tool.name} on ${on_string}: chain as alignment (clustal)">
             <filter>'clustal' in outputs</filter>
         </data>
         <data format="tabular" name="epm_list"
-              label="${tool.name} list of epms on ${on_string}">
+              label="${tool.name} on ${on_string}: list of epms">
             <filter>'epm_list' in outputs</filter>
         </data>
         <data format="tabular" name="chained_epm_list"
-              label="${tool.name} list of epms in chain on ${on_string}">
+              label="${tool.name} on ${on_string}: list of epms in chain">
             <filter>'chained_epm_list' in outputs</filter>
         </data>
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="inputA" value="tRNA_2-1.fa" />
             <param name="inputB" value="tRNA_2-2.fa" />
             <param name="outputs" value="epm_list" />
             <output name="epm_list" file="tRNA_2.epms" />
+            <output name="stdout">
+                <assert_contents>
+                    <has_text text="LCSEPM preprocessing..."/>
+                    <has_text text="#EPMs:"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
 
--- a/macros.xml	Sat Jan 21 17:38:46 2017 -0500
+++ b/macros.xml	Mon Dec 05 13:58:16 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>
 
--- a/test-data/archaea-default.stdout	Sat Jan 21 17:38:46 2017 -0500
+++ b/test-data/archaea-default.stdout	Mon Dec 05 13:58:16 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)
--- a/test-data/archaea_relplot.scr	Sat Jan 21 17:38:46 2017 -0500
+++ b/test-data/archaea_relplot.scr	Mon Dec 05 13:58:16 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);
 
--- a/test-data/haca.snoRNA-c.aln	Sat Jan 21 17:38:46 2017 -0500
+++ b/test-data/haca.snoRNA-c.aln	Mon Dec 05 13:58:16 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
--- a/test-data/haca.snoRNA-default.stdout	Sat Jan 21 17:38:46 2017 -0500
+++ b/test-data/haca.snoRNA-default.stdout	Mon Dec 05 13:58:16 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)
--- a/test-data/haca.snoRNA.aln	Sat Jan 21 17:38:46 2017 -0500
+++ b/test-data/haca.snoRNA.aln	Mon Dec 05 13:58:16 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
--- a/test-data/tRNA_2.aln	Sat Jan 21 17:38:46 2017 -0500
+++ b/test-data/tRNA_2.aln	Mon Dec 05 13:58:16 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
--- a/test-data/tRNA_2.epms	Sat Jan 21 17:38:46 2017 -0500
+++ b/test-data/tRNA_2.epms	Mon Dec 05 13:58:16 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