# HG changeset patch # User iuc # Date 1548704987 18000 # Node ID 33381b9c268c958868b00c8486c6772b750052ac # Parent dbd24c72f1669db0b2fb7880051bc02e54ab98a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 431486be049407b094d495ae4a68bf76d27fa522 diff -r dbd24c72f166 -r 33381b9c268c emboss_backtranseq.xml --- a/emboss_backtranseq.xml Mon Jan 28 11:20:53 2019 -0500 +++ b/emboss_backtranseq.xml Mon Jan 28 14:49:47 2019 -0500 @@ -1,219 +1,228 @@ - - Back translate a protein sequence - - macros.xml - - - - backtranseq -sequence '$input1' -outfile '$out_file1' -cfile $cfile -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Back translate a protein sequence + + macros.xml + + + emboss + + + backtranseq -sequence '$input1' -outfile '$out_file1' -cfile $cfile -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. class:: warningmark -The input dataset needs to be sequences. +Back-translate a protein sequence to the nucleic acid sequence it is most likely to have come from. ``backtranseq`` uses a codon usage table which gives the frequency of usage of each codon for each amino acid. For each amino acid in the input sequence, the corresponding most frequently occuring codon is used in the nucleic acid sequence that is output. ----- You can view the original documentation here_. - .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/backtranseq.html - - + .. _here: http://emboss.open-bio.org/rel/rel6/apps/backtranseq.html + + diff -r dbd24c72f166 -r 33381b9c268c test-data/emboss_backtranseq_out.fasta --- a/test-data/emboss_backtranseq_out.fasta Mon Jan 28 11:20:53 2019 -0500 +++ b/test-data/emboss_backtranseq_out.fasta Mon Jan 28 14:49:47 2019 -0500 @@ -1,30 +1,11 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -GGCACCACCTGCGGCGCCACCGGCTGCTGCACCGCCGCCGCCGCCACCGCCTGCTGCACC -ACCTGCACCACCACCACCGGCACCTGCTGCTGCACCGCCTGCGCCTGCGCCGGCGCCTGC -TGCGCCTGCGCCGGCACCACCACCACCTGCTGCACCGCCGCCACCGGCGGCTGCACCACC -ACCGCCTGCGCCTGCTGCGGCGCCTGCACCGCCGGCGCCGCCGCCACCACCTGCACCACC -GGCACCGGCTGCGCCGCCGGCTGCGCCTGCACCGCCGCCACCACCGGCGCCGCCGCCGGC -TGCGGCGGCACCACCGGCGGCTGCTGCACCGCCGGCGCCGGCACCGGCACCACCGCCTGC -TGCGGCGGCACCACCACCGGCACCGCCACCGCCGGCTGCACCGGCGCCGGCTGCGGCTGC -GGCACCTGCACCTGCACCACCGGCTGCTGCTGCACCGGCGCCACCTGCGCCGCCGCCGGC -GGCACCACCTGCGCCACCACCACCACCTGCACCTGCACCGCCTGCACCACCACCGGCGGC -GCCGCCGGCGCCTGCGGCACCACCGGCACCGGCGGCGCCGCCGGCGCCGCCACCGCCTGC -GCCGCCTGCGCCGCCGGCACCGCCTGCGGCGCCGGCACCTGCACCTGCACCTGCTGCTGC -TGCTGCTGCACCGGCGGCACCACCACCGGCTGCACCGGCGCCACCACCGCCTGCACCGGC -GGCGCCACCGCCTGCGCCGGCACCACCGGCACCGCCGCCACCGCCTGCTGCTGCACCACC -TGCGGCTGCGCCGCCTGCGCCTGCTGCGGCTGCGGCACCGCCGCCTGCACCGCCACCTGC -ACCGCCACCGCCACCGGCGCCGCCACCACCGCCACCACCACCACCTGCTGCTGCACCACC -ACCGCCACCACCGCCACCGCCACCGGCACCGCCGGCACCGCCGGCGGCACCACCTGCGGC -ACCTGCACCACCACCGCCGCCACCTGCACCACCTGCTGCACCACCACCGCCGGCTGCGCC -GCCGGCACCTGCACCACCACCACCGCCTGCACCGGCACCACCACCACCTGCGGCGCCTGC -TGCACCTGCGCCGCCACCGGCACCACCTGCGCCACCGGCACCACCTGCACCACCGCCGGC -GGCACCACCGGCACCACCACCACCGGCGGCGCCACCGCCGCCACCGCCACCGGCTGCGGC -GGCACCTGCGCCGGCACCACCACCGCCGCCACCTGCACCACCTGCGGCACCACCGGCACC -ACCACCTGCACCACCTGCACCACCGCCGCCGCCGCCACCGCCACCACCACCGCCACCACC -TGCGCCACCGGCGGCACCACCACCGCCGCCACCACCACCACCACCGGCGGCACCACCACC -GGCACCGCCTGCACCACCGGCACCACCTGCGCCGGCGGCGGCGGCTGCTGCGCCGGCACC -ACCTGCGCCACCACCGCCACCACCACCGCCTGCACCTGCACCGGCACCACCACCGGCACC -GCCACCGCCTGCGCCGGCTGCGCCGGCACCACCTGCACCACCACCACCGCCACCACCACC -ACCACCGCCGGCACCGCCACCGGCGCCACCACCACCACCGCCGCCACCACCACCGCCGCC -GCCGCCTGCGCCGCCACCACCTGCACCGCCGCCACCGGCGGCACCTGCGCCGCCGCCGCC -GCC +>Sequence_1 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +GTGAGATGCCTGAAGTACCTGCTGCTGAGCCTGCACAGACCCCAGTTCAGCTGATGGCTG +TACACCGACTGAAAGTTCCTGTGCAAGCACTGACTGAAGGCCGTGGGCCTGGAGTGCTAC +AGATTCGTGTGACTGAGCGCCAGCCTGGCCCTGATCAAGGGCAGCTTCAGCCTGCTGTGG +AAGACCCTGTGGAAGAACACCACCAGCACCAGCCTGAGCCCCCTGGTGTGCTGACTGCTG +GACACCGTGGTGATCCCCTTCGCCACCCCCAGAAACTACCTGTACGAGCTGTTCAGCCTG +TACTACATGTGATGAGTGAGACTGTGAAGCAGCTTCAGCAAGAGCTTCACCGTGTTCGAC +CTGAACGTGCACGTGCTGAGACTGTTCTGGATCATCTGCGGCCAGTTCAACCTGAGATGC +TTCTTCCTGAAGTACCTGTTCATGGTGTGATTCCTGGTGTGCACCTGCAGCGGCGCCAGC +AGCCTGTTCACCCTGTTCGTGTACAGCAGCAGCTTCATCTTCAGCATGATCCTGATCTGA +AACAACAGCAACGGCCAGAAG diff -r dbd24c72f166 -r 33381b9c268c test-data/emboss_backtranseq_out2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_backtranseq_out2.fasta Mon Jan 28 14:49:47 2019 -0500 @@ -0,0 +1,88 @@ +>Sequence_1 [1 - 51] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +GTGAGATGCCTGAAGTACCTGCTGCTGAGCCTGCACAGACCCCAGTTCAGC +>Sequence_2 [14 - 94] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +AACACCTTCTTCTGCCCCTACACCGACCACAGCTTCCCCAACGGCTTCACCCCCACCAGA +AACAGCTGCGCCAGCACCAAC +>Sequence_3 [94 - 129] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +CTGAAGGCCGTGGGCCTGGAGTGCTACAGATTCGTG +>Sequence_4 [133 - 231] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +CTGAGCGCCAGCCTGGCCCTGATCAAGGGCAGCTTCAGCCTGCTGTGGAAGACCCTGTGG +AAGAACACCACCAGCACCAGCCTGAGCCCCCTGGTGTGC +>Sequence_5 [155 - 250] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +AGCAAGGTGCACTTCCTGTACTTCGGCAGAAGATGCGGCAGAATCCAGCAGGTGAGAGTG +AGCCCCCCCTGGTTCGCCGACTACTGGATCCAGCTG +>Sequence_6 [3 - 272] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +AGCATGCCCAAGATCCCCAGCTTCGTGCCCACCCAGACCACCGTGTTCCTGATGGCCCTG +CACAGACTGGAGATCCTGGTGCAGGCCCTGATCGAGAGCGGCTGGCCCAGAGTGCTGCCC +GTGTGCATCGCCGAGAGAGTGAGCTGCCCCGACCAGAGATTCATCTTCAGCACCCTGGAG +GACGTGGTGGAGGAGTACAACAAGTACGAGAGCCTGCCCCCCGGCCTGCTGATCACCGGC +TACAGCTGCAACACCCTGAGAAACACCGCC +>Sequence_7 [235 - 309] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +CTGCTGGACACCGTGGTGATCCCCTTCGCCACCCCCAGAAACTACCTGTACGAGCTGTTC +AGCCTGTACTACATG +>Sequence_8 [288 - 335] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +ATCATCTTCCCCCTGCTGTACGTGGTGGGCAGCAGCCTGATCTTCCTG +>Sequence_9 [339 - 377] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +CAGGTGTTCTACTGCTTCAGACCCCAGTGCAGCTGCAGC +>Sequence_10 [254 - 391] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +TACCCCAGCCAGCACAGAGTGACCATCTACATGAACTACTTCCCCTTCATCATCTGCAGC +AGATTCGTGTTCAACCTGCCCCTGGCCAGCCTGCTGCTGTTCAGCACCAGCATGTTCATG +TTCCTGGGCTGCTTCGGC +>Sequence_11 [395 - 427] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +TACGCCGTGAGCCTGATCTTCGTGGTGAGCAGC +>Sequence_12 [328 - 447] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +AGCAGCTTCAGCAAGAGCTTCACCGTGTTCGACCTGAACGTGCACGTGCTGAGACTGTTC +TGGATCATCTGCGGCCAGTTCAACCTGAGATGCTTCTTCCTGAAGTACCTGTTCATGGTG +>Sequence_13 [411 - 521] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +AGCAGCCTGTTCCTGCTGAAGATCTTCATCCACGGCCTGATCTTCGGCCTGTACCTGTTC +AGAGGCCAGTTCATCATCTACAGCGTGTGCATCCAGCAGTTCTTCTACTTC +>Sequence_14 [431 - 526] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +AACATCTACAGCTGGTTCAACTTCTGGTTCGTGCTGGTGCAGGGCCCCGTGCACTACCTG +CTGTGCCTGTACACCGCCGTGCTGCTGTTCCTGGTG +>Sequence_15 [451 - 537] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +TTCCTGGTGTGCACCTGCAGCGGCGCCAGCAGCCTGTTCACCCTGTTCGTGTACAGCAGC +AGCTTCATCTTCAGCATGATCCTGATC +>Sequence_16 [531 - 487] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +AACCACACCAAGAACAAGAGAACCGCCGTGTACAAGCAGAGCAAG +>Sequence_17 [536 - 450] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +ATCAAGATCATCCTGAAGATCAAGGAGCTGCTGTACACCAACAGAGTGAACAACGAGCTG +GCCCCCGAGCAGGTGCAGACCAAGAAC +>Sequence_18 [487 - 443] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +ATCATGAACTGGCCCCTGAACAAGTACAAGCCCAAGATCAAGCCC +>Sequence_19 [468 - 439] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +ACCAGCACCAACCAGAAGCTGAACCACGAG +>Sequence_20 [439 - 410] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +ATCAACATCCTGAGAAGAAACAACGAGGAC +>Sequence_21 [446 - 405] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +ACCATGAACAAGTACTTCAAGAAGAAGCAGAGAAGACTGAAC +>Sequence_22 [401 - 372] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +CCCCACATCATCCAGAACAACCTGAGAACC +>Sequence_23 [368 - 327] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +ACCCTGAGAAGCAAGACCGTGAAGGACCTGCTGAAGGAGGAC +>Sequence_24 [426 - 292] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +GAGGAGACCACCAAGATCAAGCTGACCGCCTACTACCCCAAGCAGCCCAAGAACATGAAC +ATCGAGGTGGAGAACAGCAAGAGACTGGCCAAGGGCAGACTGAAGACCAACCTGCTGCAC +ATCATCAAGGGCAAG +>Sequence_25 [279 - 238] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +ATCGTGACCAGATGCTGCGAGGGCTACTACAACTGCATCCAG +>Sequence_26 [234 - 175] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +AGCGCCAACCAGGGCGGCGAGACCAGAACCTGCTGCATCCTGCCCCAGAGACTGCCCAAG +>Sequence_27 [334 - 158] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +AGAAAGATCAAGGACGAGCCCACCACCTACAACAAGGGCAAGATCATCCACATCGACAGC +TACGCCGTGCTGAGAAGAGTGCTGCAGCTGTACCCCGTGATCAGCAAGCCCGGCGGCAGA +GACAGCTACCTGCTGTACAGCAGCACCACCAGCAGCAAGGTGGAGAAGATGAACCTG +>Sequence_28 [275 - 120] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +CTGAGAGGCGTGGCCAAGGGCATCACCACCGTGAGCAGCAACCAGCAGACCAGAGGCGAG +AGACTGGTGCTGGTGGTGTTCTTCCACAACGTGTTCCAGAGCAGAGAGAACGAGCCCCTG +ATCAGAGCCAGAGACGCCCTGAGCTACACCAACAGA +>Sequence_29 [162 - 112] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +ACCTTCGACCAGGGCAAGAGAAGAGCCCAGCTGTACAAGCCCGTGACCCTG +>Sequence_30 [108 - 34] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +GCCAACAGATTCCAGCTGGTGCTGGCCCAGGAGTTCCTGGTGGGCGTGAAGCCCCTGGGC +AAGCTGTGGAGCGTG +>Sequence_31 [50 - 3] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +GAGAACTGCGGCCTGTGCAGAGACAAGAGAAGATACTTCAGACACAGA +>Sequence_32 [154 - 2] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +AGCGGCCAGGAGACCAGAAGCGCCATCCAGACCGGCAACACCCTGGGCCAGCCCCTGAGC +ATCAGCGCCTGCACCAGAATCAGCAGCAGATGCAAGGCCATCAGAAAGACCGTGGTGTGC +GTGGGCACCAAGGAGGGCATCCTGGGCATCGAG