- +

- - stdout_verbosity != '--quiet' - + 'clustal' in outputs @@ -234,7 +194,14 @@ - + + + + + + + + diff -r 6a79a086fa50 -r b06dc2bb3716 macros.xml --- a/macros.xml Wed Dec 28 18:53:24 2016 -0500 +++ b/macros.xml Fri Jan 13 16:49:33 2017 -0500 @@ -25,14 +25,16 @@ - - + named anchor regions per sequence. The sequence names + ('contig' names have to correspond to the fasta input + sequence names. Anchor names must be unique per sequence + and regions of the same name for different sequences + must have the same length. This constrains the alignment + to align all regions of the same name."> + + @@ -91,37 +93,176 @@ label="Temperature for RNAfold (RNAfold's -T option)" /> + + ## -------------------- scoring parameters + --indel $Scoring.indel + --indel-opening $Scoring.indel_opening + --struct-weight $Scoring.struct_weight + --tau $Scoring.tau + + #if str($Scoring.sequence_score.sequence_score_selector) == "match" + --match $Scoring.sequence_score.match + --mismatch $Scoring.sequence_score.mismatch + #elif str($Scoring.sequence_score.sequence_score_selector) == "ribosum" + --use-ribosum true + #elif str($Scoring.sequence_score.sequence_score_selector) == "ribofit" + --ribofit true + #end if + + + + ## -------------------- folding parameters + #if float($Folding.rnafold_temperature) != 37.0 + --rnafold-temperature $Folding.rnafold_temperature + #end if + + + + ## -------------------- heuristic parameters + -p $Heuristics.min_prob + + #if str($Heuristics.max_diff_mode.max_diff_mode_selector) == "off" + --max-diff -1 + #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff" + --max-diff $Heuristics.max_diff_mode.max_diff + #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-at-am" + --max-diff -1 + --max-diff-at-am $Heuristics.max_diff_mode.max_diff_at_am + #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-aln" + --max-diff $Heuristics.max_diff_mode.max_diff + --max-diff-aln '$Heuristics.max_diff_mode.max_diff_aln' + $Heuristics.max_diff_mode.max_diff_relax + #end if + + --max-diff-am $Heuristics.max_diff_am + + #if float($Heuristics.max_bps_length_ratio) > 0.0 + --max-bps-length-ratio $Heuristics.max_bps_length_ratio + #end if + + + + ## -------------------- constraint parameters + $Constraints.lonely_pairs + + #if $Constraints.maxBPspan != -1 + --maxBPspan $Constraints.maxBPspan + #end if + + $Constraints.ignore_constraints + + + + $stdout_verbosity + + #if str($stdout_verbosity) != "--quiet": + > '$stdout' + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - + label="Maximal difference for sizes of matched arcs (-1=off)" /> + 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)" /> + + + + + + + + + + + - + - - - - + stdout_verbosity != '--quiet' + + + + 'clustal' in outputs @@ -169,6 +311,8 @@ 10.1371/journal.pcbi.0030065 10.1261/rna.029041.111 + 10.1093/bioinformatics/btv185 + 10.1186/s12859-014-0404-0 diff -r 6a79a086fa50 -r b06dc2bb3716 test-data/archaea-ref.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea-ref.aln Fri Jan 13 16:49:33 2017 -0500 @@ -0,0 +1,9 @@ +CLUSTAL W --- LocARNA 1.9.0 + +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 6a79a086fa50 -r b06dc2bb3716 test-data/archaea-ref_result.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea-ref_result.aln Fri Jan 13 16:49:33 2017 -0500 @@ -0,0 +1,11 @@ +CLUSTAL W --- LocARNA 1.9.0 + + + +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- diff -r 6a79a086fa50 -r b06dc2bb3716 test-data/ferritin_human.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ferritin_human.fa Fri Jan 13 16:49:33 2017 -0500 @@ -0,0 +1,2 @@ +> human ferritin +CCAGACGUUCUUCGCCGAGAGUCGUCGGGGUUUCCUGCUUCAACAGUGCUUGGACGGAACCCGGCGCUCGUUCCCCACCCCGGCCGGCCGCCCAUAGCCAGCCCUCCGUCACCUCUUCACCGCACCCUCGGACUGCCCCAAGGCCCCCGCCGCCGCUCCAGCGCCGCGCAGCCACCGCCGCCGCCGCCGCCUCUCCUUAGUCGCCGCC diff -r 6a79a086fa50 -r b06dc2bb3716 test-data/ferritin_mouse.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ferritin_mouse.fa Fri Jan 13 16:49:33 2017 -0500 @@ -0,0 +1,2 @@ +> mouse ferritin +CAGACGUUCUCGCCCAGAGUCGCCGCGGUUUCCUGCUUCAACAGUGCUUGAACGGAACCCGGUGCUCGACCCCUCCGACCCCCGCCGGCCGCUUCGAGCCUGAGCCCUUUGCAACUUCGUCGUUCCGCCGCUCCAGCGUCGCCACCGCGCCUCGCCCCGCCGCCACC diff -r 6a79a086fa50 -r b06dc2bb3716 test-data/haca.snoRNA-1.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA-1.aln Fri Jan 13 16:49:33 2017 -0500 @@ -0,0 +1,5 @@ +ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCGAUUGGAAGACACUCUGCGACA +ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGGCAACUGUCACUCAAUGGGACA +ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGCUGCCACAGAAACAC--UGUGACUCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAGGGAUAAAUUUGGUUACAGACA +#A1 ................................................................AAAAAA...................................................................BBB +#A2 ................................................................123456...................................................................123 diff -r 6a79a086fa50 -r b06dc2bb3716 test-data/haca.snoRNA-2.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA-2.aln Fri Jan 13 16:49:33 2017 -0500 @@ -0,0 +1,3 @@ +ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGGCCCAUGGGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUAACAAUACUUACUCUCGUUGGUGAUAAGGAACA +#A1 .............................................................AAAAAA...............................................................................BBB +#A2 .............................................................123456...............................................................................123 diff -r 6a79a086fa50 -r b06dc2bb3716 test-data/haca.snoRNA-c.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA-c.aln Fri Jan 13 16:49:33 2017 -0500 @@ -0,0 +1,22 @@ +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 ............................................................ + +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 diff -r 6a79a086fa50 -r b06dc2bb3716 test-data/haca.snoRNA.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA.aln Fri Jan 13 16:49:33 2017 -0500 @@ -0,0 +1,16 @@ +CLUSTAL W --- LocARNA 1.9.0 + +ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGG +ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU +ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGC +ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCU + +ACA7 AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG +ACA30 GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG +ACA5 UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG +ACA59 GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA + +ACA7 AUUGGA--AGA---CACU-CUGCG-----ACA +ACA30 CAACUG--UCA---CUCA-AUGGG-----ACA +ACA5 GGAUAA--AUU---UGGU-UACAG-----ACA +ACA59 ACAAUACUUACUCUCGUUGGUGAUAAGGAACA diff -r 6a79a086fa50 -r b06dc2bb3716 test-data/tRNA_2.amprobs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2.amprobs Fri Jan 13 16:49:33 2017 -0500 @@ -0,0 +1,108 @@ +64 69 54 59 0.079977 +63 70 53 60 0.0158884 +63 71 53 61 0.0915855 +62 72 52 62 0.203921 +61 73 51 63 0.202155 +60 74 50 64 0.175676 +59 75 49 65 0.0815626 +39 44 33 38 0.0114647 +39 46 33 37 0.0168669 +38 47 33 38 0.0303705 +37 48 32 39 0.0111801 +37 48 31 39 0.0434528 +36 42 34 38 0.0105213 +36 42 33 37 0.0442772 +36 42 33 38 0.0150469 +36 49 30 40 0.0445378 +35 40 33 37 0.0438048 +35 40 33 38 0.0131652 +35 43 33 37 0.0482007 +35 43 33 38 0.0524118 +35 43 32 39 0.0124841 +35 44 33 38 0.0456243 +35 44 32 39 0.0111628 +35 46 33 37 0.0220704 +35 50 29 41 0.016731 +34 44 33 38 0.0275446 +34 44 32 39 0.0318614 +34 44 31 39 0.0265932 +34 45 32 39 0.0344691 +33 42 31 39 0.123358 +33 47 31 39 0.0238501 +33 48 31 39 0.207448 +33 48 30 40 0.0278532 +33 49 32 39 0.0279853 +33 49 30 40 0.0365409 +32 36 33 37 0.0659838 +32 37 33 38 0.0229925 +32 40 31 39 0.01072 +32 43 30 40 0.102105 +32 45 31 39 0.0127413 +32 45 30 40 0.0472967 +32 46 30 40 0.0814206 +32 50 29 41 0.012395 +31 38 32 39 0.0108954 +31 44 29 41 0.0212986 +31 46 29 41 0.0101171 +31 50 30 40 0.105751 +31 50 29 41 0.490312 +31 50 28 42 0.0414615 +30 38 31 39 0.10883 +30 51 29 41 0.110433 +30 51 28 42 0.628654 +30 51 27 43 0.0377824 +29 39 30 40 0.119173 +29 52 28 42 0.130101 +29 52 27 43 0.657133 +28 40 29 41 0.103713 +28 53 27 43 0.113664 +28 53 25 45 0.0385623 +27 41 28 42 0.114432 +27 54 25 45 0.651098 +26 42 27 43 0.107977 +26 55 25 45 0.119566 +26 55 23 47 0.0239947 +26 56 25 46 0.011099 +26 56 24 47 0.147548 +26 56 23 47 0.0142523 +25 57 24 47 0.0172058 +25 57 22 48 0.0238997 +24 49 25 45 0.0155194 +24 57 23 47 0.0913467 +24 57 22 48 0.640114 +23 58 22 48 0.121828 +21 60 19 51 0.071982 +20 60 18 51 0.512044 +18 63 16 53 0.410891 +17 56 18 51 0.0172516 +17 64 15 54 0.505795 +17 65 15 55 0.0373483 +16 57 17 52 0.025034 +16 65 14 55 0.456198 +15 58 16 53 0.0181784 +15 67 13 57 0.463917 +14 19 13 18 0.0159303 +14 59 15 54 0.0239939 +14 68 12 58 0.536735 +13 60 14 55 0.0191717 +12 16 11 15 0.0116456 +12 21 13 22 0.0351601 +11 17 10 16 0.0359852 +11 22 12 23 0.0512024 +11 69 11 59 0.534042 +10 14 11 15 0.0213866 +10 23 11 24 0.0659783 +10 70 10 60 0.389747 +10 72 10 62 0.247777 +9 18 9 17 0.0444132 +9 73 8 63 0.0119982 +8 19 8 18 0.0421045 +8 74 9 64 0.0471423 +8 76 8 66 0.0271918 +7 76 7 66 0.821868 +6 77 6 67 0.869036 +5 78 5 68 0.962952 +4 79 4 69 0.963261 +3 80 3 70 0.872876 +2 81 2 71 0.752745 +1 82 1 72 0.752744 diff -r 6a79a086fa50 -r b06dc2bb3716 test-data/tRNA_2.bmprobs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2.bmprobs Fri Jan 13 16:49:33 2017 -0500 @@ -0,0 +1,172 @@ +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 +8 9 0.012729 +9 8 0.010632 +9 9 0.727258 +9 10 0.0549287 +10 9 0.04195 +10 10 0.0853335 +10 11 0.0115868 +11 10 0.0364601 +11 11 0.112239 +12 10 0.011935 +12 11 0.0436248 +12 12 0.0614308 +13 11 0.0645154 +13 12 0.028434 +14 12 0.133445 +14 13 0.0169358 +15 13 0.260167 +15 14 0.0172799 +15 16 0.0124747 +16 14 0.271834 +16 15 0.0178714 +16 17 0.0141486 +17 15 0.185722 +17 16 0.0202801 +17 18 0.0184277 +18 16 0.300704 +18 17 0.0355582 +18 19 0.0165149 +19 17 0.700705 +19 18 0.0610097 +19 20 0.0138794 +20 18 0.193762 +20 19 0.11731 +20 21 0.012503 +21 19 0.633061 +21 20 0.119843 +22 20 0.625797 +22 21 0.127468 +23 20 0.0117929 +23 21 0.621337 +23 22 0.0118595 +23 24 0.0104834 +24 21 0.0184503 +24 22 0.0481581 +24 23 0.0441549 +24 25 0.0420745 +25 23 0.68405 +25 24 0.0269372 +25 26 0.0420693 +26 24 0.53624 +27 25 0.0346266 +27 26 0.120675 +28 26 0.681355 +28 27 0.0199945 +28 29 0.0196255 +29 27 0.0227404 +30 28 0.0396584 +30 29 0.0227396 +30 31 0.0165441 +31 29 0.121498 +31 32 0.114327 +32 30 0.351807 +32 31 0.0703916 +32 33 0.0332191 +33 31 0.0980398 +33 32 0.0266787 +33 34 0.0331979 +34 31 0.0122885 +34 32 0.400684 +34 33 0.0116529 +34 35 0.0331958 +35 32 0.0101403 +35 33 0.22599 +35 36 0.0332106 +36 33 0.0136772 +36 34 0.156117 +36 37 0.0332566 +37 34 0.0427905 +37 35 0.113127 +37 38 0.0933967 +38 35 0.0723242 +38 36 0.0618818 +39 34 0.0149807 +39 36 0.0997152 +39 37 0.0299675 +40 34 0.0108419 +40 35 0.01547 +40 37 0.111326 +40 38 0.0203761 +40 41 0.0196142 +41 35 0.0159003 +41 36 0.0127203 +41 38 0.149756 +42 34 0.0119499 +42 36 0.0189085 +42 37 0.010129 +42 39 0.0145996 +43 34 0.010789 +43 35 0.013731 +43 37 0.0170711 +43 38 0.0146016 +43 44 0.0354944 +44 35 0.0181452 +44 36 0.0122707 +44 38 0.0248855 +44 39 0.0183418 +44 45 0.0336616 +45 36 0.0423026 +45 39 0.0300877 +45 40 0.013096 +45 46 0.0286025 +46 37 0.0702926 +46 38 0.0130327 +46 40 0.0113529 +47 38 0.119444 +48 39 0.0264015 +48 40 0.0166626 +49 39 0.0133557 +49 40 0.309884 +50 41 0.109972 +51 41 0.0223073 +51 42 0.0365047 +52 43 0.0228365 +53 43 0.02009 +53 44 0.683193 +54 44 0.121387 +54 45 0.035521 +55 46 0.681952 +56 46 0.0343041 +56 47 0.536468 +56 48 0.0112514 +57 47 0.0531432 +57 48 0.0486503 +58 48 0.0521922 +58 49 0.632028 +59 49 0.117956 +59 50 0.628217 +60 50 0.0252284 +60 51 0.104879 +61 51 0.0460576 +61 52 0.573747 +62 52 0.165836 +62 53 0.0472354 +63 53 0.382375 +64 54 0.2672 +65 55 0.320519 +66 56 0.818192 +67 57 0.355528 +68 58 0.282881 +69 59 0.27801 +70 60 0.464549 +71 61 0.857675 +72 62 0.497193 +73 63 0.7313 +74 64 0.734773 +75 65 0.881053 +76 66 0.139472 +77 67 0.130956 +78 68 0.0370464 +79 69 0.0367371 +80 70 0.127122 +81 71 0.247251 +82 72 0.247251 +83 73 0.999955 diff -r 6a79a086fa50 -r b06dc2bb3716 test-data/tRNA_2.epms --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2.epms Fri Jan 13 16:49:33 2017 -0500 @@ -0,0 +1,4 @@ +epm_id score structure positions +0 3583 ((())) 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 +