# HG changeset patch # User iuc # Date 1548705036 18000 # Node ID dc492eb6a4fc1b8e93e2a8ed449ad21bc50a9c5c # Parent 2e0fb4bc860e492bc4f8d4b5b125c0eac2a09963 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 431486be049407b094d495ae4a68bf76d27fa522 diff -r 2e0fb4bc860e -r dc492eb6a4fc emboss_backtranseq.xml --- a/emboss_backtranseq.xml Mon Jan 28 11:22:18 2019 -0500 +++ b/emboss_backtranseq.xml Mon Jan 28 14:50:36 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 2e0fb4bc860e -r dc492eb6a4fc test-data/emboss_backtranseq_out.fasta --- a/test-data/emboss_backtranseq_out.fasta Mon Jan 28 11:22:18 2019 -0500 +++ b/test-data/emboss_backtranseq_out.fasta Mon Jan 28 14:50:36 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 2e0fb4bc860e -r dc492eb6a4fc 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 14:50:36 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