# HG changeset patch
# User rnateam
# Date 1481042354 18000
# Node ID 59055c49a11293e3f3d1eddd62bddbc97e7fca67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
diff -r 000000000000 -r 59055c49a112 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Dec 06 11:39:14 2016 -0500
@@ -0,0 +1,125 @@
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+ 1.8.12
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+ locarna
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+ stdout_verbosity != '--quiet'
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+ 'clustal' in outputs
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+ 'stockholm' in outputs
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+ 10.1371/journal.pcbi.0030065
+ 10.1261/rna.029041.111
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diff -r 000000000000 -r 59055c49a112 mlocarna.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mlocarna.xml Tue Dec 06 11:39:14 2016 -0500
@@ -0,0 +1,195 @@
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+ Multiple Alignment and Folding of RNAs
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+ macros.xml
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+ =0
+ --plfold-span $Folding.plfold_span
+ --plfold-winsize $Folding.plfold_winsize
+ #end if
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+ --rnafold-temperature $Folding.rnafold_temperature
+
+ ## -------------------- heuristic parameters
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+ -p $Heuristics.min_prob
+ --max-diff-am $Heuristics.max_diff_am
+ --max-diff $Heuristics.max_diff
+ --max-diff-at-am $Heuristics.max_diff_at_am
+ --max-bps-length-ratio $Heuristics.max_bps_length_ratio
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+ $Heuristics.alifold_consensus_dp
+
+ ## -------------------- other parameters
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+ $Other.lonely_pairs
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+ $stdout_verbosity
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+ #if str($stdout_verbosity) != "--quiet":
+ > '$stdout'
+ #end if
+ ]]>
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diff -r 000000000000 -r 59055c49a112 test-data/archaea-default.stdout
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-default.stdout Tue Dec 06 11:39:14 2016 -0500
@@ -0,0 +1,18 @@
+mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.8.12
+Copyright Sebastian Will
+
+Compute pair probs ...
+Compute pairwise alignments ...
+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)
diff -r 000000000000 -r 59055c49a112 test-data/archaea-probabilistic.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-probabilistic.aln Tue Dec 06 11:39:14 2016 -0500
@@ -0,0 +1,11 @@
+CLUSTAL W --- LocARNA 1.8.12
+
+
+
+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
diff -r 000000000000 -r 59055c49a112 test-data/archaea.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea.fa Tue Dec 06 11:39:14 2016 -0500
@@ -0,0 +1,14 @@
+>fruA
+CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG
+>fdhA
+CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG
+>vhuU
+AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU
+>hdrA
+GGCACCACUCGAAGGCUAAGCCAAAGUGGUGCU
+>vhuD
+GUUCUCUCGGGAACCCGUCAAGGGACCGAGAGAAC
+>selD
+UUACGAUGUGCCGAACCCUUUAAGGGAGGCACAUCGAAA
+>fwdB
+AUGUUGGAGGGGAACCCGUAAGGGACCCUCCAAGAU
diff -r 000000000000 -r 59055c49a112 test-data/haca.snoRNA-default.stdout
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA-default.stdout Tue Dec 06 11:39:14 2016 -0500
@@ -0,0 +1,25 @@
+mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.8.12
+Copyright Sebastian Will
+
+Compute pair probs ...
+Compute pairwise alignments ...
+Perform progressive alignment ...
+
+
+
+ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUUCGGAA-AGGGAGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30 UGGCACUUUCACAG--UUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
+ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAA--GGCUGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUGGGUGAC--CCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+#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)
diff -r 000000000000 -r 59055c49a112 test-data/haca.snoRNA.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA.fa Tue Dec 06 11:39:14 2016 -0500
@@ -0,0 +1,21 @@
+>ACA59
+GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGGCCCAUGGGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUAACAAUACUUACUCUCGUUGGUGAUAAGGAACA
+.............................................................xxxxxx...............................................................................xxx #S
+.............................................................AAAAAA...............................................................................BBB #1
+.............................................................123456...............................................................................123 #2
+
+>ACA7
+ACCUCCUGGGAUCGCAUCUGGAGAGUGCCUAGUAUUCUGCCAGCUUCGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCGAUUGGAAGACACUCUGCGACA
+...........................................................xxxxxx...................................................................xxx #S
+...........................................................AAAAAA...................................................................BBB #1
+...........................................................123456...................................................................123 #2
+>ACA5
+UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAAGGCUGCCACAGAAACACUGUGACUCAUGGGCCCUGUUCCUGUGUCCCAGGCUCAGGGAUAAAUUUGGUUACAGACA
+..............................................................xxxxxx............................................................xxx #S
+..............................................................AAAAAA............................................................BBB #1
+..............................................................123456............................................................123 #2
+>ACA30
+UGGCACUUUCACAGUUCCUUCCCCAGGCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAACCCUUGAUUGUAUUCUUGCCCUGGGAUUAUACCAGUGGCAACUGUCACUCAAUGGGACA
+..........................................................xxxxxx..........................................................xxx #S
+..........................................................AAAAAA..........................................................BBB #1
+..........................................................123456..........................................................123 #2
diff -r 000000000000 -r 59055c49a112 test-data/tRNA_5.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_5.fa Tue Dec 06 11:39:14 2016 -0500
@@ -0,0 +1,10 @@
+>D10744
+GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
+>AF008220
+GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA
+>Z11880
+GCCUUCCUAGCUCAGUGGUAGAGCGCACGGCUUUUAACCGUGUGGUCGUGGGUUCGAUCCCCACGGAAGGCG
+>X02172
+GCCUUUAUAGCUUAGUGGUAAAGCGAUAAACUGAAGAUUUAUUUACAUGUAGUUCGAUUCUCAUUAAGGGCA
+>M68929
+GCGGAUAUAACUUAGGGGUUAAAGUUGCAGAUUGUGGCUCUGAAAACACGGGUUCGAAUCCCGUUAUUCGCC