# HG changeset patch
# User bgruening
# Date 1724093551 0
# Node ID 7d63908343c3e05c30fc3f0eac22f13deb822486
# Parent e84d1fc87829aa5e6f1695822a92b9183fbbda8b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 94c141a71ef115279f1090f782b6f5cdeea9c277
diff -r e84d1fc87829 -r 7d63908343c3 locarna_reliability_profile.xml
--- a/locarna_reliability_profile.xml Mon Dec 05 14:29:00 2022 +0000
+++ b/locarna_reliability_profile.xml Mon Aug 19 18:52:31 2024 +0000
@@ -6,11 +6,8 @@
macros.xml
-
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output_format == 'pdf'
-
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output_format == 'png'
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+
write_rscript is True
@@ -201,4 +145,4 @@
-
+
\ No newline at end of file
diff -r e84d1fc87829 -r 7d63908343c3 macros.xml
--- a/macros.xml Mon Dec 05 14:29:00 2022 +0000
+++ b/macros.xml Mon Aug 19 18:52:31 2024 +0000
@@ -1,7 +1,7 @@
- 1.9.2.3
- 1
- 21.09
+ 2.0.1
+ 0
+ 23.0
diff -r e84d1fc87829 -r 7d63908343c3 test-data/archaea-default.stdout
--- a/test-data/archaea-default.stdout Mon Dec 05 14:29:00 2022 +0000
+++ b/test-data/archaea-default.stdout Mon Aug 19 18:52:31 2024 +0000
@@ -1,9 +1,13 @@
-mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0
-Copyright Sebastian Will
-
-Compute pair probs ...
-Compute pairwise alignments ...
-Perform progressive alignment ...
+mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 2.0.1
+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 ((.(((((((((...(((.................))).))))))))))). (-31.36 = -20.01 + -11.34)
+Results written to target directory /tmp/tmpstsz4a83/job_working_directory/000/2/working/mlocarna_results.
diff -r e84d1fc87829 -r 7d63908343c3 test-data/archaea-probabilistic.aln
--- a/test-data/archaea-probabilistic.aln Mon Dec 05 14:29:00 2022 +0000
+++ b/test-data/archaea-probabilistic.aln Mon Aug 19 18:52:31 2024 +0000
@@ -1,11 +1,10 @@
-CLUSTAL W --- LocARNA 1.9.0
-
+CLUSTAL W --- LocARNA 2.0.1
-selD UUACGAUGUGCCGAACCCUU------------UAAGGGAGGCACAUCGAAA
-vhuU AGC-UCACAACCGAACCCAU-------------UUGGGAGGUUGUGAG-CU
-fwdB AUG-UUGGAGGGGAACCCGU-------------AAGGGACCCUCCAAG-AU
-hdrA GGC-ACC-ACUCGAAGGCU--------------AAGCCAAAGU-GGUG-CU
-vhuD GUU-CUC-UCGGGAACCCGU------------CAAGGGACCGA-GAGA-AC
-fdhA CGC-CACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGG-CG
-fruA CC-UCG--AGGGGAACCCGA-------------AAGGGACCC--GAGA-GG
+vhuU AGC-UCACAACCGAACCCA-----U---U-----UGGGAGGUUGUGA-GCU
+fwdB AUG-UUGGAGGGGAACCCG-----U---A-----AGGGACCCUCCAA-GAU
+selD UUACGAUGUGCCGAACCCU-----U--UA-----AGGGAGGCACAUCGAAA
+hdrA GGC-ACC-ACUCGAAGGCU---------A-----AGCCAAAGU-GGU-GCU
+vhuD GUU-CUC-UCGGGAACCCG-----U--CA-----AGGGACCGA-GAG-AAC
+fruA CC-UCGA--GGGGAACCCG-----A---A-----AGGGACCC--GAGA-GG
+fdhA CGC-CACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUG-GCG
diff -r e84d1fc87829 -r 7d63908343c3 test-data/archaea-ref_result.aln
--- a/test-data/archaea-ref_result.aln Mon Dec 05 14:29:00 2022 +0000
+++ b/test-data/archaea-ref_result.aln Mon Aug 19 18:52:31 2024 +0000
@@ -1,5 +1,4 @@
-CLUSTAL W --- LocARNA 1.9.0
-
+CLUSTAL W --- LocARNA 2.0.1
vhuU AG-CUCACAACCGAACCC-AU------------UUGGGAGGUUGUGAGCU-
diff -r e84d1fc87829 -r 7d63908343c3 test-data/archaea_relplot.scr
--- a/test-data/archaea_relplot.scr Mon Dec 05 14:29:00 2022 +0000
+++ b/test-data/archaea_relplot.scr Mon Aug 19 18:52:31 2024 +0000
@@ -1,4 +1,4 @@
-pdf("/tmp/tmp5yxSuG/files/000/dataset_2.dat",width=12,height=4,version="1.4")
+pdf("/tmp/tmpewnb251n/job_working_directory/000/2/outputs/dataset_a612ea0e-aca2-4d90-987a-39141bc61f36.dat",width=12,height=4,version="1.4")
rel <- read.table("mlocarna_results/results/result.bmreliability");
seqrel <- rel[[2]]
@@ -112,8 +112,8 @@
if (0!=1) {
- on <- c(0,4,33,44,49);
- off <- c(3,20,43,48,51);
+ on <- c(0,33);
+ off <- c(20,51);
if (length(on)>0) {
for (i in 1:length(on)) {
@@ -123,8 +123,8 @@
### draw on/off values
if (0) {
- lines(c(1,1+len),c(0.0355791,0.0355791),lty=2,lwd=1)
- lines(c(1,1+len),c(0.702675,0.702675),lty=2,lwd=1)
+ lines(c(1,1+len),c(0.0139513,0.0139513),lty=2,lwd=1)
+ lines(c(1,1+len),c(0.656017,0.656017),lty=2,lwd=1)
}
}
diff -r e84d1fc87829 -r 7d63908343c3 test-data/haca.snoRNA-c.aln
--- a/test-data/haca.snoRNA-c.aln Mon Dec 05 14:29:00 2022 +0000
+++ b/test-data/haca.snoRNA-c.aln Mon Aug 19 18:52:31 2024 +0000
@@ -1,4 +1,4 @@
-CLUSTAL W --- LocARNA 1.9.2.3
+CLUSTAL W --- LocARNA 2.0.1
ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG
ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG
diff -r e84d1fc87829 -r 7d63908343c3 test-data/haca.snoRNA-default.stdout
--- a/test-data/haca.snoRNA-default.stdout Mon Dec 05 14:29:00 2022 +0000
+++ b/test-data/haca.snoRNA-default.stdout Mon Aug 19 18:52:31 2024 +0000
@@ -1,10 +1,20 @@
-mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0
-Copyright Sebastian Will
-
-Compute pair probs ...
-Compute pairwise alignments ...
-Perform progressive alignment ...
+mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 2.0.1
-alifold .((((((((........((((.(((((((......))))))).))))......))..)))))).............(((((((...((......((((((((((((.....)))))))))
- ))).........)).))).))))......... (-62.29 = -34.50 + -27.79)
+ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUUCGGAA-AGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30 UGGCACUUUCACAG--UUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG
+ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAA--GGCUGCCACAGAAACAC--UGUGAC-----UCAUG-GGCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG--CCCAUGGGUGA-CCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+#A1 ................................................................AAAAAA..................................................
+#A2 ................................................................123456..................................................
+
+ACA7 AUUGGA-----AGACACU-CUGCG-----ACA
+ACA30 CAACUG-----UCACUCA-AUGGG-----ACA
+ACA5 GGAUAA-----AUUUGGU-UACAG-----ACA
+ACA59 ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
+#A1 .............................BBB
+#A2 .............................123
+
+alifold .((((((..........((((..(((((........)))))..))))..........)))))).............((((((.............((((((((..........)))).))
+ ))..............)).))))......... (-53.08 = -26.63 + -26.46)
+Results written to target directory /tmp/tmpstsz4a83/job_working_directory/000/4/working/mlocarna_results.
diff -r e84d1fc87829 -r 7d63908343c3 test-data/haca.snoRNA.aln
--- a/test-data/haca.snoRNA.aln Mon Dec 05 14:29:00 2022 +0000
+++ b/test-data/haca.snoRNA.aln Mon Aug 19 18:52:31 2024 +0000
@@ -1,4 +1,4 @@
-CLUSTAL W --- LocARNA 1.9.2.3
+CLUSTAL W --- LocARNA 2.0.1
ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG
ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG
diff -r e84d1fc87829 -r 7d63908343c3 test-data/tRNA_2.aln
--- a/test-data/tRNA_2.aln Mon Dec 05 14:29:00 2022 +0000
+++ b/test-data/tRNA_2.aln Mon Aug 19 18:52:31 2024 +0000
@@ -1,4 +1,4 @@
-CLUSTAL W --- LocARNA 1.9.2.3 --- Score: 2587
+CLUSTAL W --- LocARNA 2.0.1 --- Score: 2587
D10744 GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
AF008220 GGAGGAUUAGC--UCAGCUGGGAGAGCAUCUGCCUUA-------CAAGCAGAGGGUCGGCG-GUUCGAGCCCGUCAUCCUCCA
diff -r e84d1fc87829 -r 7d63908343c3 test-data/tRNA_2.amprobs
--- a/test-data/tRNA_2.amprobs Mon Dec 05 14:29:00 2022 +0000
+++ b/test-data/tRNA_2.amprobs Mon Aug 19 18:52:31 2024 +0000
@@ -1,108 +1,185 @@
-64 69 54 59 0.079977
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-63 71 53 61 0.0915855
-62 72 52 62 0.203921
-61 73 51 63 0.202155
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diff -r e84d1fc87829 -r 7d63908343c3 test-data/tRNA_2.bmprobs
--- a/test-data/tRNA_2.bmprobs Mon Dec 05 14:29:00 2022 +0000
+++ b/test-data/tRNA_2.bmprobs Mon Aug 19 18:52:31 2024 +0000
@@ -1,172 +1,204 @@
-1 1 0.247253
-2 2 0.247252
-3 3 0.127121
-4 4 0.0367335
-5 5 0.0369676
-6 6 0.129988
-7 7 0.156077
-8 8 0.835935
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-27 25 0.0346266
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-30 28 0.0396584
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