| Previous changeset 2:94b0468f0db8 (2017-01-21) Next changeset 4:6e20ad2c8752 (2024-08-19) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042 |
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modified:
locarna_multiple.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 |
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removed:
locarna.tar.bz2 |
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| diff -r 94b0468f0db8 -r 7554c0df9139 locarna.tar.bz2 |
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| Binary file locarna.tar.bz2 has changed |
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| diff -r 94b0468f0db8 -r 7554c0df9139 locarna_multiple.xml --- a/locarna_multiple.xml Sat Jan 21 17:38:28 2017 -0500 +++ b/locarna_multiple.xml Mon Dec 05 14:28:49 2022 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="locarna_multiple" name="LocARNA Multiple Aligner" version="@VERSION@.1"> +<tool id="locarna_multiple" name="LocARNA Multiple Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description> Multiple Alignment and Folding of RNAs (mlocarna) </description> @@ -22,7 +22,8 @@ #end if --tgtdir mlocarna_results - --width 60 + ## maybe reenable later? see https://github.com/s-will/LocARNA/issues/77 + ## --width 60 ## -------------------- alignment mode and specific options # @@ -65,10 +66,9 @@ @STDOUT_ARGS@ - #if 'clustal_strict' in str($outputs).split(",") + #if 'strict' in str($outputs).split(",") && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln #end if - ]]></command> <inputs> @@ -93,8 +93,7 @@ help="Note that local alignment mode usually requires to turn off the 'max-diff' heuristic (maximal difference for alignment traces)." > - <option value="global_locarna">Global alignment - (LocARNA)</option> + <option value="global_locarna">Global alignment (LocARNA)</option> <option value="local_locarna">Local alignment (LocARNA)</option> <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option> <option value="sparse">Global fast alignment (SPARSE)</option> @@ -129,46 +128,33 @@ <expand macro="common_heuristic_parameters_sparse" /> </section> </when> - </conditional> - - <param name="outputs" type="select" display="checkboxes" multiple="True" + <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output options"> - <option value="clustal_strict" selected="True">Output alignment - in ClustalW format</option> - <option value="clustal" selected="False">Output alignment - in constraint-annotated ClustalW format</option> - <option value="stockholm" selected="False">Output - alignment in Stockholm format</option> - <option value="pp" selected="False">Output - alignment in LocARNA's PP 2.0 format</option> - <option value="mlocarna_results" selected="False"> - Output LocARNA results archive (tar.gz)</option> + <option value="strict" selected="true">Alignment in ClustalW format</option> + <option value="clustal" selected="false">Alignment in constraint-annotated ClustalW format</option> + <option value="stockholm" selected="false">Alignment in Stockholm format</option> + <option value="pp" selected="false">Alignment in LocARNA's PP 2.0 format</option> + <option value="mlocarna_results" selected="false">LocARNA results archive (tar.gz)</option> </param> - <param name="stdout_verbosity" type="select" label="Standard output verbosity"> - <option value="--quiet">Don't report standard - output</option> + <option value="--quiet">Don't report standard output</option> <option value="">Non verbose</option> <option value="--verbose">Verbose</option> <option value="--moreverbose">More verbose</option> </param> - <section name="Scoring" title="Scoring parameters"> <expand macro="common_scoring_parameters" /> </section> - <section name="Folding" title="RNA folding parameters"> <expand macro="plfolding_parameters" /> <expand macro="common_folding_parameters" /> <expand macro="alifold_consensus_parameter" /> </section> - <section name="Heuristics" title="Heuristic parameters"> <expand macro="common_heuristic_parameters" /> <expand macro="max_diff_parameters_aln" /> </section> - <section name="Constraints" title="Constraint parameters"> <expand macro="bed_anchors" /> <expand macro="common_constraint_parameters" /> @@ -180,33 +166,59 @@ </outputs> <tests> - <test> + <test expect_num_outputs="3"> <param name="input_data" value="archaea.fa" /> <param name="stdout_verbosity" value="" /> <param name="max_diff_mode_selector" value="max-diff" /> <param name="max_diff" value="20" /> - <output name="stdout" file="archaea-default.stdout" /> + <param name="outputs" value="clustal,strict"/> + <output name="stdout" file="archaea-default.stdout" lines_diff="2" /> + <output name="clustal"> + <assert_contents> + <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/> + </assert_contents> + </output> + <output name="clustal_strict"> + <assert_contents> + <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs="2"> <param name="input_data" value="haca.snoRNA.fa" /> <param name="stdout_verbosity" value="" /> - <output name="stdout" file="haca.snoRNA-default.stdout" /> + <output name="stdout" file="haca.snoRNA-default.stdout" lines_diff="2" /> + <output name="clustal_strict"> + <assert_contents> + <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs="2"> <param name="input_data" value="archaea.fa" /> <param name="stdout_verbosity" value="" /> <param name="outputs" value="clustal" /> <param name="alignment_mode_selector" value="probabilistic" /> - <output name="clustal" file="archaea-probabilistic.aln" /> + <output name="stdout"> + <assert_contents> + <has_text text="mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA @TOOL_VERSION@"/> + </assert_contents> + </output> + <output name="clustal" file="archaea-probabilistic.aln" lines_diff="2"/> </test> - <test> + <test expect_num_outputs="2"> <param name="input_data" value="archaea.fa" /> <param name="stdout_verbosity" value="" /> <param name="outputs" value="clustal" /> <param name="max_diff_mode_selector" value="max-diff-aln" /> <param name="max_diff_aln" value="archaea-ref.aln" /> <param name="max_diff" value="2" /> - <output name="clustal" file="archaea-ref_result.aln" /> + <output name="stdout"> + <assert_contents> + <has_text text="mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA @TOOL_VERSION@"/> + </assert_contents> + </output> + <output name="clustal" file="archaea-ref_result.aln" lines_diff="2"/> </test> </tests> |
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| diff -r 94b0468f0db8 -r 7554c0df9139 macros.xml --- a/macros.xml Sat Jan 21 17:38:28 2017 -0500 +++ b/macros.xml Mon Dec 05 14:28:49 2022 +0000 |
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| b'@@ -1,9 +1,12 @@\n <macros>\n- <token name="@VERSION@">1.9.0</token>\n+ <token name="@TOOL_VERSION@">1.9.2.3</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n+ <token name="@PROFILE@">21.09</token>\n \n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="@VERSION@">locarna</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">locarna</requirement>\n+ <requirement type="package" version="4.2.2">r-base</requirement> \n </requirements>\n </xml>\n \n@@ -46,15 +49,15 @@\n </xml>\n \n <xml name="common_scoring_parameters">\n- <param name="struct_weight" argument="struct-weight"\n+ <param argument="--struct-weight"\n label="Structure weight" type="integer" \n value="200" min="0" max="800" />\n- <param name="indel_opening" argument="indel-opening"\n+ <param argument="--indel-opening"\n label="Indel opening score" type="integer"\n value="-500" max="0" min="-1500" />\n- <param argument="indel" label="Indel score" type="integer" \n+ <param argument="--indel" label="Indel score" type="integer" \n value="-350" min="-1000" max="0" />\n- <param argument="tau" type="integer" value="50"\n+ <param argument="--tau" type="integer" value="50"\n min="0" max="200"\n label="Sequence contribution at structure match in percent"/> \n \n@@ -78,17 +81,17 @@\n </xml>\n \n <xml name="plfolding_parameters">\n- <param name="plfold_span" argument="--plfold-span" \n+ <param argument="--plfold-span" \n type="integer" value="150" min="-1" max="400" \n label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />\n \n- <param name="plfold_winsize" argument="--plfold-winsize"\n+ <param argument="--plfold-winsize"\n type="integer" value="300" min="-1" max="800" \n label="Window size for local folding" />\n </xml>\n \n <xml name="common_folding_parameters">\n- <param name="rnafold_temperature" argument="rnafold-temperature"\n+ <param argument="rnafold-temperature"\n type="float" value="37.0" min="10" max="50"\n label="Temperature for RNAfold (RNAfold\'s -T option)" />\n </xml>\n@@ -147,16 +150,18 @@\n \n </token>\n \n- <token name="@CONSTRAINT_ARGS@">\n- ## -------------------- constraint parameters\n- $Constraints.lonely_pairs\n-\n+ <token name="@CONSTRAINT_ARGS_WOLP@">\n #if $Constraints.maxBPspan != -1\n --maxBPspan $Constraints.maxBPspan\n #end if\n \n $Constraints.ignore_constraints\n </token>\n+ <token name="@CONSTRAINT_ARGS@">\n+ ## -------------------- constraint parameters\n+ $Constraints.lonely_pairs\n+ @CONSTRAINT_ARGS_WOLP@\n+ </token>\n \n <token name="@STDOUT_ARGS@">\n $stdout_verbosity\n@@ -171,7 +176,7 @@\n label="Restrict alignable positions by maximum difference" \n help="(max-diff*)">\n <option value="off">Off</option>\n- <option value="max-diff" selected="True">Maximal difference of aligned positions</option>\n+ <option value="max-diff" selected="true">Maximal difference of aligned positions</option>\n <option value="max-diff-at-am">Maximal difference of aligned positions at arc matches</option> \n <yield />\n </param>\n@@ -180,12 +185,12 @@\n <xml name="max_diff_parameters_standard_cases">\n <when value="off" />\n <when value="max-diff">\n- <param name="max_diff" argument="max-diff" type="integer"\n+ <param argument="--max-diff" type="integer"\n value="60" min="-1" max="300"\n label="Maximal difference of aligned positions" />\n </when>\n <when value="max-diff-at-am">\n- '..b'hold"\n+ <param argument="--prob_basepair_in_loop_threshold"\n type="float" value="0.01" min="0.0" max="1.0" \n label="Probability threshold for base pairs in loops" />\n </xml>\n \n <xml name="alifold_consensus_parameter">\n- <param name="alifold_consensus_dp" argument="alifold-consensus-dp" \n+ <param argument="--alifold-consensus-dp" \n type="boolean" checked="False" \n truevalue="--alifold-consensus-dp" falsevalue=""\n label="Compute consensus dot plot by alifold" />\n </xml>\n \n- <xml name="common_constraint_parameters">\n- <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" \n- checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" />\n- <param name="maxBPspan" argument="--maxBPspan" \n+ <xml name="common_constraint_parameters_woLP">\n+ <yield/>\n+ <param argument="--maxBPspan" \n type="integer" value="-1" min="-1" max="400" \n label="Maximum basepair span by RNAfold; -1 for arbitrary span" />\n- <param name="ignore_constraints" argument="ignore-constraints"\n+ <param argument="--ignore-constraints"\n type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue=""\n help="Ignore all anchor and structure constraints given\n in the fasta(-ish) input." />\n </xml>\n \n+ <xml name="common_constraint_parameters">\n+ <expand macro="common_constraint_parameters_woLP">\n+ <param argument="--noLP" name="lonely_pairs" type="boolean" truevalue="" falsevalue="--noLP" \n+ checked="true" label="Allow lonely base-pairs"/>\n+ </expand>\n+ </xml>\n+\n <xml name="standard_outupt">\n- <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">\n+ <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout">\n <filter>stdout_verbosity != \'--quiet\'</filter>\n </data>\n </xml>\n@@ -299,25 +308,25 @@\n <xml name="mlocarna_outputs">\n <expand macro="standard_outupt" />\n <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln"\n- label="${tool.name} alignment (annotated clustal) on ${on_string}">\n+ label="${tool.name} on ${on_string}: alignment (annotated clustal)">\n <filter>\'clustal\' in outputs</filter>\n </data>\n <data format="clustal" name="clustal_strict" \n from_work_dir="mlocarna_results/results/result.strict-aln"\n- label="${tool.name} alignment (clustal) on ${on_string}">\n- <filter>\'clustal_strict\' in outputs</filter>\n+ label="${tool.name} on ${on_string}: alignment (clustal)">\n+ <filter>\'strict\' in outputs</filter>\n </data>\n <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk"\n- label="${tool.name} alignment (stockholm) on ${on_string}">\n+ label="${tool.name} on ${on_string}: alignment (stockholm)">\n <filter>\'stockholm\' in outputs</filter>\n </data>\n <data format="txt" name="pp"\n from_work_dir="mlocarna_results/results/result.pp"\n- label="${tool.name} alignment (PP 2.0) on ${on_string}">\n+ label="${tool.name} on ${on_string}: alignment (PP 2.0)">\n <filter>\'pp\' in outputs</filter>\n </data>\n <data format="tar.gz" name="mlocarna_results_tgz"\n- label="${tool.name} results archive on ${on_string}">\n+ label="${tool.name} on ${on_string}: results archive">\n <filter>\'mlocarna_results\' in outputs</filter>\n </data>\n </xml>\n@@ -330,8 +339,5 @@\n <citation type="doi">10.1186/s12859-014-0404-0</citation>\n </citations>\n </xml>\n-\n-\n-\n </macros>\n \n' |
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| diff -r 94b0468f0db8 -r 7554c0df9139 test-data/archaea-default.stdout --- a/test-data/archaea-default.stdout Sat Jan 21 17:38:28 2017 -0500 +++ b/test-data/archaea-default.stdout Mon Dec 05 14:28:49 2022 +0000 |
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| @@ -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) |
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| diff -r 94b0468f0db8 -r 7554c0df9139 test-data/archaea_relplot.scr --- a/test-data/archaea_relplot.scr Sat Jan 21 17:38:28 2017 -0500 +++ b/test-data/archaea_relplot.scr Mon Dec 05 14:28:49 2022 +0000 |
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| @@ -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); |
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| diff -r 94b0468f0db8 -r 7554c0df9139 test-data/haca.snoRNA-c.aln --- a/test-data/haca.snoRNA-c.aln Sat Jan 21 17:38:28 2017 -0500 +++ b/test-data/haca.snoRNA-c.aln Mon Dec 05 14:28:49 2022 +0000 |
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| @@ -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 |
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| diff -r 94b0468f0db8 -r 7554c0df9139 test-data/haca.snoRNA-default.stdout --- a/test-data/haca.snoRNA-default.stdout Sat Jan 21 17:38:28 2017 -0500 +++ b/test-data/haca.snoRNA-default.stdout Mon Dec 05 14:28:49 2022 +0000 |
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| @@ -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) |
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| diff -r 94b0468f0db8 -r 7554c0df9139 test-data/haca.snoRNA.aln --- a/test-data/haca.snoRNA.aln Sat Jan 21 17:38:28 2017 -0500 +++ b/test-data/haca.snoRNA.aln Mon Dec 05 14:28:49 2022 +0000 |
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| @@ -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 |
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| diff -r 94b0468f0db8 -r 7554c0df9139 test-data/tRNA_2.aln --- a/test-data/tRNA_2.aln Sat Jan 21 17:38:28 2017 -0500 +++ b/test-data/tRNA_2.aln Mon Dec 05 14:28:49 2022 +0000 |
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| @@ -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 |
| b |
| diff -r 94b0468f0db8 -r 7554c0df9139 test-data/tRNA_2.epms --- a/test-data/tRNA_2.epms Sat Jan 21 17:38:28 2017 -0500 +++ b/test-data/tRNA_2.epms Mon Dec 05 14:28:49 2022 +0000 |
| b |
| @@ -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 |