| Previous changeset 2:e66514da3a99 (2022-12-05) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 94c141a71ef115279f1090f782b6f5cdeea9c277 |
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modified:
locarna_exparnap.xml macros.xml test-data/archaea-default.stdout test-data/archaea-probabilistic.aln test-data/archaea-ref_result.aln 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.amprobs test-data/tRNA_2.bmprobs |
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| diff -r e66514da3a99 -r a80f279b4ad0 locarna_exparnap.xml --- a/locarna_exparnap.xml Mon Dec 05 13:58:16 2022 +0000 +++ b/locarna_exparnap.xml Mon Aug 19 18:53:00 2024 +0000 |
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| b'@@ -2,25 +2,18 @@\n <description>\n Pairwise Simultaneous Matching and Folding of RNAs (ExpaRNA-P)\n </description>\n-\n <macros>\n <import>macros.xml</import>\n </macros>\n-\n- <expand macro="requirements" />\n-\n- <expand macro="stdio" />\n-\n- <expand macro="version" />\n-\n+ <expand macro="requirements"/>\n+ <expand macro="stdio"/>\n+ <expand macro="version"/>\n <command><![CDATA[\n exparna_p\n-\n \'$inputA\'\n \'$inputB\'\n \n- ## -------------------- scoring parameters\n- #\n+ ## -------------------- scoring parameters -------------#\n $Scoring.no_stacking\n --alpha_1 $Scoring.alpha_1\n --alpha_2 $Scoring.alpha_2\n@@ -35,8 +28,7 @@\n \n @CONSTRAINT_ARGS@\n @FOLDING_ARGS@\n- ## -------------------- other parameters\n- #\n+ ## -------------------- other parameters---------------- #\n #if str($Other.subopt.subopt_selector) == "on"\n --diff-to-opt-score $Other.subopt.diff_to_opt_score\n --number-of-EPMs $Other.subopt.number_of_EPMs\n@@ -49,7 +41,7 @@\n $Other.no_chaining\n --out-min-prob $Other.out_min_prob\n \n- ## -------------------- output\n+ ## -------------------- output ---------------- #\n \n #if \'postscript\' in str($outputs).split(",")\n --output-ps\n@@ -79,7 +71,7 @@\n \n @STDOUT_ARGS@\n \n- ## -------------------- post processing\n+ ## -------------------- post processing --------------#\n \n #if \'anchors-pp\' in str($outputs).split(",")\n && mv anchors_pp_A.pp \'$anchors_ppA\'\n@@ -89,161 +81,95 @@\n ]]></command>\n \n <inputs>\n- <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"\n- help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"\n- />\n- <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"\n- help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"\n- />\n-\n- <param name="outputs" type="select" display="checkboxes" multiple="true"\n- label="Output options">\n- <option value="postscript" selected="false">Best EPM chain\n- as colored postscript</option>\n- <option value="anchors-fasta" selected="false">Fasta with anchor\n- constraints from chaining</option>\n- <option value="anchors-pp" selected="false">LocARNA PP\n- files merging input PPs and anchor constraints from\n- chaining</option>\n- <option value="clustal" selected="false">Chain as\n- alignment in Clustal format</option>\n+ <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A" help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"/>\n+ <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"/>\n+ <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output options">\n+ <option value="postscript" selected="false">Best EPM chain as colored postscript</option>\n+ <option value="anchors-fasta" selected="false">Fasta with anchor constraints from chaining</option>\n+ <option value="anchors-pp" selected="false">LocARNA PP files merging input PPs and anchor constraints from chaining</option>\n+ <option value="clustal" selected="false">Chain as alignment in Clustal format</option>\n <option value="epm_list" selected="false">List of the found EPMs</option>\n- <option value="chained_epm_list" selected="false">List of\n- EPMs in the best chain</option>\n+ <option value="chained_epm_list" selected="false">List of EPMs in the best chain</option>\n </param>\n-\n <param name="stdout_verbosity" type="select" label="Standard output verbosity">\n- <option value="--quiet">Don\'t report standard\n- output</option>\n+ <option value="--q'..b'value="30" min="0" max="1000" label="Minimum score of EPM" />\n+ <param argument="--inexact-struct-match" type="boolean" truevalue="--inexact-struct-match" falsevalue="" label="Allow inexact structure matches"/>\n+ <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)"/>\n+ <param argument="--no-chaining" type="boolean" truevalue="" falsevalue="--no-chaining" checked="true" label="Find best overall chain by chaining"/>\n+ <param argument="--out-min-prob" type="float" value="0.0005" min="0" max="1" label="Minimal probability in output (min-prob overrides if smaller)"/>\n </section>\n </inputs>\n \n <outputs>\n <expand macro="standard_outupt" />\n- <data format="ps" name="ps_fileA"\n- label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">\n+ <data format="ps" name="ps_fileA" label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">\n <filter>\'postscript\' in outputs</filter>\n </data>\n- <data format="ps" name="ps_fileB"\n- label="${tool.name} on ${on_string}: chain in RNA 2 (postscript)">\n+ <data format="ps" name="ps_fileB" label="${tool.name} on ${on_string}: chain in RNA 2 (postscript)">\n <filter>\'postscript\' in outputs</filter>\n </data>\n- <data format="txt" name="anchors_fasta"\n- label="${tool.name} on ${on_string}: anchor constraints from chain (fasta)">\n+ <data format="txt" name="anchors_fasta" label="${tool.name} on ${on_string}: anchor constraints from chain (fasta)">\n <filter>\'anchors-fasta\' in outputs</filter>\n </data>\n- <data format="txt" name="anchors_ppA"\n- label="${tool.name} on ${on_string}: anchors for RNA 1 (pp)">\n+ <data format="txt" name="anchors_ppA" label="${tool.name} on ${on_string}: anchors for RNA 1 (pp)">\n <filter>\'anchors-pp\' in outputs</filter>\n </data>\n- <data format="txt" name="anchors_ppB"\n- label="${tool.name} on ${on_string}: anchors for RNA 2 (pp)">\n+ <data format="txt" name="anchors_ppB" label="${tool.name} on ${on_string}: anchors for RNA 2 (pp)">\n <filter>\'anchors-pp\' in outputs</filter>\n </data>\n- <data format="clustal" name="clustal"\n- label="${tool.name} on ${on_string}: chain as alignment (clustal)">\n+ <data format="clustal" name="clustal" label="${tool.name} on ${on_string}: chain as alignment (clustal)">\n <filter>\'clustal\' in outputs</filter>\n </data>\n- <data format="tabular" name="epm_list"\n- label="${tool.name} on ${on_string}: list of epms">\n+ <data format="tabular" name="epm_list" label="${tool.name} on ${on_string}: list of epms">\n <filter>\'epm_list\' in outputs</filter>\n </data>\n- <data format="tabular" name="chained_epm_list"\n- label="${tool.name} on ${on_string}: list of epms in chain">\n+ <data format="tabular" name="chained_epm_list" label="${tool.name} on ${on_string}: list of epms in chain">\n <filter>\'chained_epm_list\' in outputs</filter>\n </data>\n </outputs>\n \n <tests>\n <test expect_num_outputs="2">\n- <param name="inputA" value="tRNA_2-1.fa" />\n- <param name="inputB" value="tRNA_2-2.fa" />\n- <param name="outputs" value="epm_list" />\n- <output name="epm_list" file="tRNA_2.epms" />\n+ <param name="inputA" value="tRNA_2-1.fa"/>\n+ <param name="inputB" value="tRNA_2-2.fa"/>\n+ <param name="outputs" value="epm_list"/>\n+ <output name="epm_list" file="tRNA_2.epms"/>\n <output name="stdout">\n <assert_contents>\n <has_text text="LCSEPM preprocessing..."/>\n' |
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| diff -r e66514da3a99 -r a80f279b4ad0 macros.xml --- a/macros.xml Mon Dec 05 13:58:16 2022 +0000 +++ b/macros.xml Mon Aug 19 18:53:00 2024 +0000 |
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| @@ -1,7 +1,7 @@ <macros> - <token name="@TOOL_VERSION@">1.9.2.3</token> - <token name="@VERSION_SUFFIX@">1</token> - <token name="@PROFILE@">21.09</token> + <token name="@TOOL_VERSION@">2.0.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.0</token> <xml name="requirements"> <requirements> |
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| diff -r e66514da3a99 -r a80f279b4ad0 test-data/archaea-default.stdout --- a/test-data/archaea-default.stdout Mon Dec 05 13:58:16 2022 +0000 +++ b/test-data/archaea-default.stdout Mon Aug 19 18:53:00 2024 +0000 |
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| @@ -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. |
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| diff -r e66514da3a99 -r a80f279b4ad0 test-data/archaea-probabilistic.aln --- a/test-data/archaea-probabilistic.aln Mon Dec 05 13:58:16 2022 +0000 +++ b/test-data/archaea-probabilistic.aln Mon Aug 19 18:53:00 2024 +0000 |
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| @@ -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 |
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| diff -r e66514da3a99 -r a80f279b4ad0 test-data/archaea-ref_result.aln --- a/test-data/archaea-ref_result.aln Mon Dec 05 13:58:16 2022 +0000 +++ b/test-data/archaea-ref_result.aln Mon Aug 19 18:53:00 2024 +0000 |
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| @@ -1,5 +1,4 @@ -CLUSTAL W --- LocARNA 1.9.0 - +CLUSTAL W --- LocARNA 2.0.1 vhuU AG-CUCACAACCGAACCC-AU------------UUGGGAGGUUGUGAGCU- |
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| diff -r e66514da3a99 -r a80f279b4ad0 test-data/archaea_relplot.scr --- a/test-data/archaea_relplot.scr Mon Dec 05 13:58:16 2022 +0000 +++ b/test-data/archaea_relplot.scr Mon Aug 19 18:53:00 2024 +0000 |
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| @@ -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) } } |
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| diff -r e66514da3a99 -r a80f279b4ad0 test-data/haca.snoRNA-c.aln --- a/test-data/haca.snoRNA-c.aln Mon Dec 05 13:58:16 2022 +0000 +++ b/test-data/haca.snoRNA-c.aln Mon Aug 19 18:53:00 2024 +0000 |
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| @@ -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 |
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| diff -r e66514da3a99 -r a80f279b4ad0 test-data/haca.snoRNA-default.stdout --- a/test-data/haca.snoRNA-default.stdout Mon Dec 05 13:58:16 2022 +0000 +++ b/test-data/haca.snoRNA-default.stdout Mon Aug 19 18:53:00 2024 +0000 |
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| @@ -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. |
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| diff -r e66514da3a99 -r a80f279b4ad0 test-data/haca.snoRNA.aln --- a/test-data/haca.snoRNA.aln Mon Dec 05 13:58:16 2022 +0000 +++ b/test-data/haca.snoRNA.aln Mon Aug 19 18:53:00 2024 +0000 |
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| @@ -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 |
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| diff -r e66514da3a99 -r a80f279b4ad0 test-data/tRNA_2.aln --- a/test-data/tRNA_2.aln Mon Dec 05 13:58:16 2022 +0000 +++ b/test-data/tRNA_2.aln Mon Aug 19 18:53:00 2024 +0000 |
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| @@ -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 |
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| diff -r e66514da3a99 -r a80f279b4ad0 test-data/tRNA_2.amprobs --- a/test-data/tRNA_2.amprobs Mon Dec 05 13:58:16 2022 +0000 +++ b/test-data/tRNA_2.amprobs Mon Aug 19 18:53:00 2024 +0000 |
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| @@ -1,108 +1,185 @@ -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 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| b |
| diff -r e66514da3a99 -r a80f279b4ad0 test-data/tRNA_2.bmprobs --- a/test-data/tRNA_2.bmprobs Mon Dec 05 13:58:16 2022 +0000 +++ b/test-data/tRNA_2.bmprobs Mon Aug 19 18:53:00 2024 +0000 |
| b |
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