Galaxy |

Changeset 4:0db979fead3a (2017-06-01)

Previous changeset 3:b408e5a8b137 (2016-07-06) Next changeset 5:c6334cb383ff (2020-10-08)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit f0e5f4748034bc0f1faafcec65bffa34b64a4781

modified:
transdecoder.xml

removed:
test-data/gencode/test.fa.transdecoder.mRNA
test-data/raw/test.fa.transdecoder.mRNA
test-data/strand/test.fa.transdecoder.mRNA
test-data/top/test.fa.transdecoder.mRNA
tool_dependencies.xml

diff -r b408e5a8b137 -r 0db979fead3a test-data/gencode/test.fa.transdecoder.mRNA
--- a/test-data/gencode/test.fa.transdecoder.mRNA Wed Jul 06 11:30:14 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,266 +0,0 @@\n->CUFF.36.1|m.5 CUFF.36.1|g.5 ORF CUFF.36.1|g.5 CUFF.36.1|m.5 type:complete len:169 (+) CUFF.36.1:895-1401(+)\n-TGACTAAGTGGCAATGATGCTCCTAATGAAACCACTGATCCTCGATCATCAGCAGTAGTA\n-TCAATAGCAGCATCAGCACCGTTAGACAGCTGTTTTTCTAAACCATTCAATGATTCATCT\n-GAAAAACGTGAACCCACTTTCGAATAGTGCTTTTCAAATTTCTTTCCCGTAATTAAGGAA\n-AGTAAATCCATGTGCAGTTAGTATTGAAAAGGAAAGAATAAATAAAAGTGGGTCAAAAGT\n-AACGCCAAACAAACGAAGGTTATCGAAATATATGCGAAGGAGAGATTTATATACTAGTCA\n-AATTTAAACAGCTGAGATTGCTTTAGTCATCGCGTTGTTCCAGATCGTGAACGAAAACAC\n-CGATTCGCTCGCTAAAGTAGATACGAAATGTCCAGCAGATTTTGCTTAATTAAAACATAA\n-ATATTGATGAGCAAGAGCAGCTCGTTATAAATCAGACCTCCAAGGATTTTATCAACTACT\n-CAACTGGTTATGTGAATAATGACTCAGTTAAATATTAAATGTACTCTAAACGGTTATCAT\n-ACAATTTATTAGGAGGATTATACCAGCTAGTAGGAATTTAACCATTTCAAATTTAAACCT\n-CTTTTTTTTCGTAACTTGGGGTCGTCATAATGAATAATTCTGTTTGTCGAATTTGAAGGG\n-AAAAACACACTTGTTATCTAATTCCAAAAAAAAATAAAAAATTTTTAAAAATTAGTGGGG\n-TTTTTTTTTCACCAATGTCTAATGATGTGTGATTTAAAAAAAAACGTGTGTAACGCATTG\n-TAGTATTACTTACCTTTGCATGATTAAAAGTATATGTTGATATCGACTATTTAGAGTACT\n-GTGCGACACATTACCCTATGTTTCCCACTCTTAATCACCAAAAATTTTTTCCGAATGTCG\n-CAAGACTCAGAATCGTTCATCCGGCAACTGTTTAAGGCATTTACGGATTTTAGTACTGAC\n-GTTGAGTCACTTAGAGGATTTTTAACGCCAGATTATCGACAGCTTGTCGATGGACGTGAA\n-TTGACACTTGACGATTTTATTTCTCATGCCAAAGCACTACGTACCCATCTTCATCGGCTC\n-GACATCAACGTTCAACAAATTGTCTGTCAAGGTAACAAGGCTGCCACTGTGCATATTGCC\n-CATGCGATACGTTCCTCTGGCGAGTCCAGCAGAATCAAAGTCATTGCATTTTACAGTTTT\n-AAAGACGGGCGTATTTCTTTGATCGATGAGTTGACGTACGTTCTTGAAGGTGGTAATGCA\n-GACAGAGAGCTTGGATCAGTACAATGACTTCAATTACCTTGACACTGCATTGCCCACGTT\n-ATTCAACGTCCATCAGGAACCGGACAAATTATTCAGAGTCCTTTTGAACTACTTCATAAT\n-TTTACAAATATTCAAGTGTAATTCGTAATATAATCAGTTTTATTCATCTTCGTTGTCTAA\n-AACTTTTATGTGCTGCAATATTTGGGGAATCTCGATTTGACATAATGATCCCAGTGCC\n->CUFF.4.1|m.7 CUFF.4.1|g.7 ORF CUFF.4.1|g.7 CUFF.4.1|m.7 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+)\n-CTCTTTTTAATATTTTACCGATGAGATTGCTATTATTAGTTACGTTGCTATCTATCGTTG\n-GTTACACTAATCAGTTGCTTTCCAACTGACCTCGAAGACGCTCCAGCTGTAATCTGGGTA\n-GCCCAATTTCCTCCAGATAACACTACACAGCACTATGAATTCAGATATATCGTAAATGAA\n-TTATATAATGCTAGCAAGATGACTGCATTAATGAACCATATATATATCGATAATCCGCTT\n-ATAAGCAATTCAACTAATAACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTAT\n-AATGACGGAGAGATTTCCAGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGAT\n-GATGCTACATGGATAATCAACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAG\n-AAGCGAGACCGATACACCACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGT\n-GACACTGGAGCCAATGCTGTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGA\n-GGTGATTGGGGGGGG\n->CUFF.51.1|m.1 CUFF.51.1|g.1 ORF CUFF.51.1|g.1 CUFF.51.1|m.1 type:complete len:372 (+) CUFF.51.1:2632-3747(+)\n-CGACGTTAATAAAATATTTAACAAAGCCTTTAAAAAATTAACGATAGCTAGTCAAAGGAA\n-GCTTAACGCGTATTCAGCCTCATTAAGACAATCAGGAAGCTTTTTTTTACCATCAGCATA\n-TACCTCTAACCCTTTGATTTATTTTTATATCTCGAGATTTCGTTCGTTATTTTATAGGTC\n-GTTTCGATAAGACCTTAATACAATCTGATTTAGTGGTTGTTTAAGATTTCGGAAAAGCCT\n-TTTTTTCAAAAAAAGTTTTCCAGTTATTGTTTCATTATTTCTAATTGATTTACTGAAGAA\n-TTGTTATAACCTAAAGATGGCACTTATGTTATCCAGGATTCCACGTCGTTTTTTTTTCTT\n-ATTTTTAACGGTCGGCTTGATTGCTGGCGCGTTTCTATACTCGTTGATATATTTTGTGGA\n-CGTTGATTTGGTGTCGAAGGTTAACCAGTTGTATGATCAGCAAATTGCACCCATGCTCTC\n-CGATGCTATTGGCACTCCATCCGTTAATCACTCGTTTGAGTTGGCGCCGTTAGACTCTCA\n-TTTGGTGGCCACAAGCACTACATTCCACGAGGCGTCATACGAGTCAGAGCCTCAGCAAAA\n-TCCTGCCAGTCAAAATATTGTCTTATTACTAGTTAGTGATGGACACACTTCTTACAATAA\n-TGGAGCTAATACGTTTGAAGAAGCTATACAGAACAGAGTTGACTATAGTACCAAACAAAA\n-CTACAACTTTGAGTATGTCAATGTTACTGGCCTCCCTATTCCCGCCGTTTGGTCCAAGAT\n-GCCCGCCGTCTTACAAACTATGAAGAAATACCCCAAAGCGGAATGGATCTGGTTGTTGGA\n-TCAGGATGCAATTATTACTAATACCCATCTTTCCCTTCAAGACTCCTTTTTGAAACCTGA\n-GAACTTGCAAAAGACCTTAATTACTAATACCATCCTCACTAAACGGCCTATAAATGCTAA\n-CGGGGATTTGCGTTATACACCAAGTAATTATAGTTTAAAAGATATCGAAAATCTCATGGT\n-CATAATCTCACAGGATCACAATGGATTAAACGCAGGTAGTATCTTGTTCCGTAATTCACC\n-TGCTACTGCCTTGTTTTTGGATATTTGGACAGATCCTGTTGTTGCAGAATGTGCGAAAGC\n-CAATAATGAACAAGACATGCTTGGATATTTGATTTCTAAGCATTCACAACTTGCTTCGCT\n-GGTTGGCCTTATTCCTCAAAGAAAAATAAATGCTTTTCACGAAGGTCCGGAAAATATGGA\n-ATGGCAAAAAGGTGATTTGGTAATTCACTTTGCTGGATGTTGGGTTGAAAACCGCTGCGA\n-TGAACTATGGCAAAAGTTTTACGCCTTGATTGACTAAGTTGCTTATTCATTATATCCGTC\n-TGTTTAATTTGTTTGTGTTTTAAAAAATTTTATATATATAAACAAAGCGCCGTATAATTT\n-TCCGTCAATCTTCCTTTCTTTATCTGAATCTCTAA'..b'GGACAAGA\n-ATATATACCCCAATACTCTGTCTGTTTTACGTACTCGTGCTTCTGGTTTTGGTATCAAAA\n-TTGAATTAGACAATATCACTCCTGAACTCATTACGAAGTCTGCTAAGCATGTTTTTGGTA\n-TCTTTGTGCAATACCCAGCGGCGGATGGCTCTATTTTTGACTATGGTCATTTAGCTGCTA\n-CAGCACGCTCTTTTAATATGCACGTCGTAGCTGCCACCGATTTACTAGCTCTCACTATTT\n-TGAAATCGCCTGGGGAATGGGGTGCCGATGTTGCTGTTGGTTCCACTCAGCGCTTTGGTC\n-TGCCCATGGGCTATGGTGGCCCCCATGCCGGATTCTTTGCTTGTAGTGAAGAATTTAAAC\n-GAAAGATACCCGGTCGTCTTATTGGTCTCAGCAAAGATCGTTTAGAAAATCCCGCATACC\n-GGTTGGCTCTTCAAACAAGAGAACAACATATTCGTCGTGAAAAGGCTACAAGTAACATTT\n-GCACGGCTCAAGCTTTGTTAGCCAATATGTCTGCATTCTATGCTATTTACCATGGGCCAA\n-ATGGTCTCCAAGAAATTGCAAACCGTATTTACGCTAGTACCTCCTTCTTAAAATCTGCTT\n-TGGAATCTTCAGGATATAAAATTGTTAATAAAAGTCATTTCTTTGACACATTAACTATCG\n-AAGTTGAGTCGGCTGACAAAGTTCTTGCGAAAGCACTTGATCACGGTTACAATTTAAGAA\n-AGGTTGATGATTCACATGTTGGTCTTTCATTGGACGAGACCGTTTGCGATAAAGATATTC\n-AAGCTTTGTTTAGCATCTTTAATATAAATAAGAGTGTTGATCAGTATTATATGGAAATTG\n-CAACGTCGGAACCTAATGGAAATTCTGCTTCAACAGTCGATAATCTCAGCATTTGTTCTC\n-TTCCTGAAAACTTTAGACGAACAACCCTCTATTTACAACATCCCGTGTTTAACAGATACC\n-ATTCGGAAACTGAACTTATGCGTTATATTCATCATTTGCAGTCGAAGGATCTATCTTTAG\n-CTCATGCCATGACCCCATTGGGTTCGTGCACAATGAAGTTGAATGCTGTCACCGAAATGA\n-TGCCAATCACAAATCCATTATTTGCCAACATTCATCCATATGTTCCAGAGGAACAAGCTA\n-AAGGTTATCGTCATGTTATCGAAGATTTGCAGTTAATGTTAACGACCATCACCGGCTTTG\n-ATGCTGCATGCTTTCAACCAAATTCGGGAGCCGCTGGAGAATACACTGGCTTAAGTGTTA\n-TTCGAGCATATCAGCGGTCTATTGGTCAAGGTCATCGCAATATTTGCTTAATTCCTGTTT\n-CGGCTCACGGTACTAATCCAGCTTCAGCTGCTATGGCTGGGTTTACTGTTATTCCTGTAA\n-AATGTCTCAATAACGGTTATTTGGATATGCAAGACTTAAAAGAAAAGGCCTCTAAACACG\n-CCGACAAGTTAGCTGCCTTTATGGTAACTTATCCTAGTACTTTTGGCATTTTTGAGCCTG\n-ATGTTAAGGAAGCTTTGGAAGTAATTCACGAACATGGTGGTCAGGTTTACTTTGATGGTG\n-CTAACATGAATGCAATGGTTGGTTTATGCAAGGCTGGTGATATTGGTGCTGATGTTTGTC\n-ACTTAAATCTTCATAAGACATTTTGCATTCCTCACGGCGGTGGCGGTCCTGGTGTAGGTC\n-CTATTTGTGTAAAAAAGCATCTTGCTGATTTCCTACCATCTCATCCTGTAGTTTCATGCG\n-GCGGTAAGAATGGTATCACATCTGTTAGCTCTTCTCCTTTTGGCTCTGCTGGTATTTTAC\n-CTATCTCATGGGCATACATGAGAATGATGGGACTTGCCGGTTTGCGTGACGCTTCCAAAG\n-CCGCTCTGTTAAATGCCAATTATATGGCCAAGCGCCTGTCATCTCATTATAAACTTGTTT\n-ACACTAATAAGAACAACCTCTGTGCTCATGAGTTTATTCTAGATGCTCGCGAATTTAAAG\n-CTACTGCGGGTGTAGATGCAACTGATATAGCTAAACGTTTGCAAGATTACAGTTTCCATG\n-CACCAACTCTTTCCTGGCCTATTGCTAATACACTGATGATTGAGCCTACCGAGTCTGAGA\n-GTATGTATGAGATGGACCGCTTCTGTGATGCTTTAATTTCTATTCGACAAGAAATTCGTG\n-AAATTGAAGAAGGTCTCCAGCCTAAGGACAATAACCTGCTCGTTAATGCTCCCCACCCTC\n-AAAAGGACATTGCATCTGAGAAATGGGATCGTCCTTATACTCGAGAGCGGGCTGTCTATC\n-CTGTGCCTCTTTTAAAGGAACGGAAATTCTGGCCTAGCGTTGCTCGATTAGATGATGCGT\n-ACGGTGACAAGAACTTATTTTGTACTTGTTCCCCAGTTGTTTAGCGGTCAAAAAGAGCTC\n-ACCTGCTAGATTACTTCAACCTTTTCCCAGTTAAGTTCAACCTAATTTTTACTCCATTTG\n-GTAGTTCGTTCAACACCAATTCCCACGTTTATATATAGACCAATTTTTTACTACATCTTG\n-TTAGACAATTCTTTCCGTTATCACTTTTTCGAATTTTTTTTAATTACGTTTTAATTTTGA\n-AGGTTAGAATTATCCTTTGCTGGAACATGAGGTTTTCAACAACCTTTTTTTAATCTGATA\n-ATCTAATTTTGCTAGTCATATAATTGCGACTTTCTGATAAAAACATTACCTATACTTTAT\n-AAATATGTCGTTTTTAAATATTAACTCCTATGTCTTACTTGCATCCTTGAAATTTACGAC\n-TAGAAATTTGGTGCTTTGGATTTTCGTTACATTAAGTAAGGCCATTGAATCGATATGACA\n-CGTAAATGTTAAATTTCAAAATATTTTGGAGAGCACCATGTATAATTTAAATATACGAAT\n-TTTTTCCTTTAAATTTGTGGTTCTTTTTTAAAAAATATCAAGACGAGTACTCGATTACTC\n-GTAAGTATTCAAG\n->CUFF.9.1|m.8 CUFF.9.1|g.8 ORF CUFF.9.1|g.8 CUFF.9.1|m.8 type:complete len:156 (+) CUFF.9.1:173-640(+)\n-AGCGAAACAAACAAATCACGTTATAGACGGTGGCAGGGCCATAAAAGGTATTCCCTCGCT\n-TTAAAAAGAAACAATGTCAAAAAGCTTTCTTTATAAACTATTGGAAGATTGAAGACATTA\n-AAGAAGAAAAGTCCTGCTTACCCTTGGACTTTTTTCAGCAGTTTTCATTGCCATGCCTAT\n-CAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAACCTGAATT\n-TCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTACTTTTCGG\n-TTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCCATTATGGG\n-TGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCATATGGAAT\n-TTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGAGCCATCTT\n-TCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGTACTTTACT\n-TGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTATGGAAAACA\n-AATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAGTTGATTTAACTGATCAAAGT\n-GAGGATTTTCACACACATTTTCAGAGTACTTGGAACGTGCCGAGCTGATTAAAAAACACC\n-GGTATTAACAAAAAATTTTATTTATGAAGCAATACGCTATTTCGTTATGAGAAACTTGAT\n-TCAATGAAACTATTATAAACCTTA\n'

diff -r b408e5a8b137 -r 0db979fead3a test-data/raw/test.fa.transdecoder.mRNA
--- a/test-data/raw/test.fa.transdecoder.mRNA Wed Jul 06 11:30:14 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,266 +0,0 @@\n->CUFF.36.1|m.4 CUFF.36.1|g.4 ORF CUFF.36.1|g.4 CUFF.36.1|m.4 type:complete len:131 (+) CUFF.36.1:895-1287(+)\n-TGACTAAGTGGCAATGATGCTCCTAATGAAACCACTGATCCTCGATCATCAGCAGTAGTA\n-TCAATAGCAGCATCAGCACCGTTAGACAGCTGTTTTTCTAAACCATTCAATGATTCATCT\n-GAAAAACGTGAACCCACTTTCGAATAGTGCTTTTCAAATTTCTTTCCCGTAATTAAGGAA\n-AGTAAATCCATGTGCAGTTAGTATTGAAAAGGAAAGAATAAATAAAAGTGGGTCAAAAGT\n-AACGCCAAACAAACGAAGGTTATCGAAATATATGCGAAGGAGAGATTTATATACTAGTCA\n-AATTTAAACAGCTGAGATTGCTTTAGTCATCGCGTTGTTCCAGATCGTGAACGAAAACAC\n-CGATTCGCTCGCTAAAGTAGATACGAAATGTCCAGCAGATTTTGCTTAATTAAAACATAA\n-ATATTGATGAGCAAGAGCAGCTCGTTATAAATCAGACCTCCAAGGATTTTATCAACTACT\n-CAACTGGTTATGTGAATAATGACTCAGTTAAATATTAAATGTACTCTAAACGGTTATCAT\n-ACAATTTATTAGGAGGATTATACCAGCTAGTAGGAATTTAACCATTTCAAATTTAAACCT\n-CTTTTTTTTCGTAACTTGGGGTCGTCATAATGAATAATTCTGTTTGTCGAATTTGAAGGG\n-AAAAACACACTTGTTATCTAATTCCAAAAAAAAATAAAAAATTTTTAAAAATTAGTGGGG\n-TTTTTTTTTCACCAATGTCTAATGATGTGTGATTTAAAAAAAAACGTGTGTAACGCATTG\n-TAGTATTACTTACCTTTGCATGATTAAAAGTATATGTTGATATCGACTATTTAGAGTACT\n-GTGCGACACATTACCCTATGTTTCCCACTCTTAATCACCAAAAATTTTTTCCGAATGTCG\n-CAAGACTCAGAATCGTTCATCCGGCAACTGTTTAAGGCATTTACGGATTTTAGTACTGAC\n-GTTGAGTCACTTAGAGGATTTTTAACGCCAGATTATCGACAGCTTGTCGATGGACGTGAA\n-TTGACACTTGACGATTTTATTTCTCATGCCAAAGCACTACGTACCCATCTTCATCGGCTC\n-GACATCAACGTTCAACAAATTGTCTGTCAAGGTAACAAGGCTGCCACTGTGCATATTGCC\n-CATGCGATACGTTCCTCTGGCGAGTCCAGCAGAATCAAAGTCATTGCATTTTACAGTTTT\n-AAAGACGGGCGTATTTCTTTGATCGATGAGTTGACGTACGTTCTTGAAGGTGGTAATGCA\n-GACAGAGAGCTTGGATCAGTACAATGACTTCAATTACCTTGACACTGCATTGCCCACGTT\n-ATTCAACGTCCATCAGGAACCGGACAAATTATTCAGAGTCCTTTTGAACTACTTCATAAT\n-TTTACAAATATTCAAGTGTAATTCGTAATATAATCAGTTTTATTCATCTTCGTTGTCTAA\n-AACTTTTATGTGCTGCAATATTTGGGGAATCTCGATTTGACATAATGATCCCAGTGCC\n->CUFF.4.1|m.5 CUFF.4.1|g.5 ORF CUFF.4.1|g.5 CUFF.4.1|m.5 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+)\n-CTCTTTTTAATATTTTACCGATGAGATTGCTATTATTAGTTACGTTGCTATCTATCGTTG\n-GTTACACTAATCAGTTGCTTTCCAACTGACCTCGAAGACGCTCCAGCTGTAATCTGGGTA\n-GCCCAATTTCCTCCAGATAACACTACACAGCACTATGAATTCAGATATATCGTAAATGAA\n-TTATATAATGCTAGCAAGATGACTGCATTAATGAACCATATATATATCGATAATCCGCTT\n-ATAAGCAATTCAACTAATAACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTAT\n-AATGACGGAGAGATTTCCAGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGAT\n-GATGCTACATGGATAATCAACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAG\n-AAGCGAGACCGATACACCACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGT\n-GACACTGGAGCCAATGCTGTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGA\n-GGTGATTGGGGGGGG\n->CUFF.51.1|m.2 CUFF.51.1|g.2 ORF CUFF.51.1|g.2 CUFF.51.1|m.2 type:complete len:347 (+) CUFF.51.1:317-1357(+)\n-CGACGTTAATAAAATATTTAACAAAGCCTTTAAAAAATTAACGATAGCTAGTCAAAGGAA\n-GCTTAACGCGTATTCAGCCTCATTAAGACAATCAGGAAGCTTTTTTTTACCATCAGCATA\n-TACCTCTAACCCTTTGATTTATTTTTATATCTCGAGATTTCGTTCGTTATTTTATAGGTC\n-GTTTCGATAAGACCTTAATACAATCTGATTTAGTGGTTGTTTAAGATTTCGGAAAAGCCT\n-TTTTTTCAAAAAAAGTTTTCCAGTTATTGTTTCATTATTTCTAATTGATTTACTGAAGAA\n-TTGTTATAACCTAAAGATGGCACTTATGTTATCCAGGATTCCACGTCGTTTTTTTTTCTT\n-ATTTTTAACGGTCGGCTTGATTGCTGGCGCGTTTCTATACTCGTTGATATATTTTGTGGA\n-CGTTGATTTGGTGTCGAAGGTTAACCAGTTGTATGATCAGCAAATTGCACCCATGCTCTC\n-CGATGCTATTGGCACTCCATCCGTTAATCACTCGTTTGAGTTGGCGCCGTTAGACTCTCA\n-TTTGGTGGCCACAAGCACTACATTCCACGAGGCGTCATACGAGTCAGAGCCTCAGCAAAA\n-TCCTGCCAGTCAAAATATTGTCTTATTACTAGTTAGTGATGGACACACTTCTTACAATAA\n-TGGAGCTAATACGTTTGAAGAAGCTATACAGAACAGAGTTGACTATAGTACCAAACAAAA\n-CTACAACTTTGAGTATGTCAATGTTACTGGCCTCCCTATTCCCGCCGTTTGGTCCAAGAT\n-GCCCGCCGTCTTACAAACTATGAAGAAATACCCCAAAGCGGAATGGATCTGGTTGTTGGA\n-TCAGGATGCAATTATTACTAATACCCATCTTTCCCTTCAAGACTCCTTTTTGAAACCTGA\n-GAACTTGCAAAAGACCTTAATTACTAATACCATCCTCACTAAACGGCCTATAAATGCTAA\n-CGGGGATTTGCGTTATACACCAAGTAATTATAGTTTAAAAGATATCGAAAATCTCATGGT\n-CATAATCTCACAGGATCACAATGGATTAAACGCAGGTAGTATCTTGTTCCGTAATTCACC\n-TGCTACTGCCTTGTTTTTGGATATTTGGACAGATCCTGTTGTTGCAGAATGTGCGAAAGC\n-CAATAATGAACAAGACATGCTTGGATATTTGATTTCTAAGCATTCACAACTTGCTTCGCT\n-GGTTGGCCTTATTCCTCAAAGAAAAATAAATGCTTTTCACGAAGGTCCGGAAAATATGGA\n-ATGGCAAAAAGGTGATTTGGTAATTCACTTTGCTGGATGTTGGGTTGAAAACCGCTGCGA\n-TGAACTATGGCAAAAGTTTTACGCCTTGATTGACTAAGTTGCTTATTCATTATATCCGTC\n-TGTTTAATTTGTTTGTGTTTTAAAAAATTTTATATATATAAACAAAGCGCCGTATAATTT\n-TCCGTCAATCTTCCTTTCTTTATCTGAATCTCTAAT'..b'GGACAAGA\n-ATATATACCCCAATACTCTGTCTGTTTTACGTACTCGTGCTTCTGGTTTTGGTATCAAAA\n-TTGAATTAGACAATATCACTCCTGAACTCATTACGAAGTCTGCTAAGCATGTTTTTGGTA\n-TCTTTGTGCAATACCCAGCGGCGGATGGCTCTATTTTTGACTATGGTCATTTAGCTGCTA\n-CAGCACGCTCTTTTAATATGCACGTCGTAGCTGCCACCGATTTACTAGCTCTCACTATTT\n-TGAAATCGCCTGGGGAATGGGGTGCCGATGTTGCTGTTGGTTCCACTCAGCGCTTTGGTC\n-TGCCCATGGGCTATGGTGGCCCCCATGCCGGATTCTTTGCTTGTAGTGAAGAATTTAAAC\n-GAAAGATACCCGGTCGTCTTATTGGTCTCAGCAAAGATCGTTTAGAAAATCCCGCATACC\n-GGTTGGCTCTTCAAACAAGAGAACAACATATTCGTCGTGAAAAGGCTACAAGTAACATTT\n-GCACGGCTCAAGCTTTGTTAGCCAATATGTCTGCATTCTATGCTATTTACCATGGGCCAA\n-ATGGTCTCCAAGAAATTGCAAACCGTATTTACGCTAGTACCTCCTTCTTAAAATCTGCTT\n-TGGAATCTTCAGGATATAAAATTGTTAATAAAAGTCATTTCTTTGACACATTAACTATCG\n-AAGTTGAGTCGGCTGACAAAGTTCTTGCGAAAGCACTTGATCACGGTTACAATTTAAGAA\n-AGGTTGATGATTCACATGTTGGTCTTTCATTGGACGAGACCGTTTGCGATAAAGATATTC\n-AAGCTTTGTTTAGCATCTTTAATATAAATAAGAGTGTTGATCAGTATTATATGGAAATTG\n-CAACGTCGGAACCTAATGGAAATTCTGCTTCAACAGTCGATAATCTCAGCATTTGTTCTC\n-TTCCTGAAAACTTTAGACGAACAACCCTCTATTTACAACATCCCGTGTTTAACAGATACC\n-ATTCGGAAACTGAACTTATGCGTTATATTCATCATTTGCAGTCGAAGGATCTATCTTTAG\n-CTCATGCCATGACCCCATTGGGTTCGTGCACAATGAAGTTGAATGCTGTCACCGAAATGA\n-TGCCAATCACAAATCCATTATTTGCCAACATTCATCCATATGTTCCAGAGGAACAAGCTA\n-AAGGTTATCGTCATGTTATCGAAGATTTGCAGTTAATGTTAACGACCATCACCGGCTTTG\n-ATGCTGCATGCTTTCAACCAAATTCGGGAGCCGCTGGAGAATACACTGGCTTAAGTGTTA\n-TTCGAGCATATCAGCGGTCTATTGGTCAAGGTCATCGCAATATTTGCTTAATTCCTGTTT\n-CGGCTCACGGTACTAATCCAGCTTCAGCTGCTATGGCTGGGTTTACTGTTATTCCTGTAA\n-AATGTCTCAATAACGGTTATTTGGATATGCAAGACTTAAAAGAAAAGGCCTCTAAACACG\n-CCGACAAGTTAGCTGCCTTTATGGTAACTTATCCTAGTACTTTTGGCATTTTTGAGCCTG\n-ATGTTAAGGAAGCTTTGGAAGTAATTCACGAACATGGTGGTCAGGTTTACTTTGATGGTG\n-CTAACATGAATGCAATGGTTGGTTTATGCAAGGCTGGTGATATTGGTGCTGATGTTTGTC\n-ACTTAAATCTTCATAAGACATTTTGCATTCCTCACGGCGGTGGCGGTCCTGGTGTAGGTC\n-CTATTTGTGTAAAAAAGCATCTTGCTGATTTCCTACCATCTCATCCTGTAGTTTCATGCG\n-GCGGTAAGAATGGTATCACATCTGTTAGCTCTTCTCCTTTTGGCTCTGCTGGTATTTTAC\n-CTATCTCATGGGCATACATGAGAATGATGGGACTTGCCGGTTTGCGTGACGCTTCCAAAG\n-CCGCTCTGTTAAATGCCAATTATATGGCCAAGCGCCTGTCATCTCATTATAAACTTGTTT\n-ACACTAATAAGAACAACCTCTGTGCTCATGAGTTTATTCTAGATGCTCGCGAATTTAAAG\n-CTACTGCGGGTGTAGATGCAACTGATATAGCTAAACGTTTGCAAGATTACAGTTTCCATG\n-CACCAACTCTTTCCTGGCCTATTGCTAATACACTGATGATTGAGCCTACCGAGTCTGAGA\n-GTATGTATGAGATGGACCGCTTCTGTGATGCTTTAATTTCTATTCGACAAGAAATTCGTG\n-AAATTGAAGAAGGTCTCCAGCCTAAGGACAATAACCTGCTCGTTAATGCTCCCCACCCTC\n-AAAAGGACATTGCATCTGAGAAATGGGATCGTCCTTATACTCGAGAGCGGGCTGTCTATC\n-CTGTGCCTCTTTTAAAGGAACGGAAATTCTGGCCTAGCGTTGCTCGATTAGATGATGCGT\n-ACGGTGACAAGAACTTATTTTGTACTTGTTCCCCAGTTGTTTAGCGGTCAAAAAGAGCTC\n-ACCTGCTAGATTACTTCAACCTTTTCCCAGTTAAGTTCAACCTAATTTTTACTCCATTTG\n-GTAGTTCGTTCAACACCAATTCCCACGTTTATATATAGACCAATTTTTTACTACATCTTG\n-TTAGACAATTCTTTCCGTTATCACTTTTTCGAATTTTTTTTAATTACGTTTTAATTTTGA\n-AGGTTAGAATTATCCTTTGCTGGAACATGAGGTTTTCAACAACCTTTTTTTAATCTGATA\n-ATCTAATTTTGCTAGTCATATAATTGCGACTTTCTGATAAAAACATTACCTATACTTTAT\n-AAATATGTCGTTTTTAAATATTAACTCCTATGTCTTACTTGCATCCTTGAAATTTACGAC\n-TAGAAATTTGGTGCTTTGGATTTTCGTTACATTAAGTAAGGCCATTGAATCGATATGACA\n-CGTAAATGTTAAATTTCAAAATATTTTGGAGAGCACCATGTATAATTTAAATATACGAAT\n-TTTTTCCTTTAAATTTGTGGTTCTTTTTTAAAAAATATCAAGACGAGTACTCGATTACTC\n-GTAAGTATTCAAG\n->CUFF.9.1|m.6 CUFF.9.1|g.6 ORF CUFF.9.1|g.6 CUFF.9.1|m.6 type:complete len:156 (+) CUFF.9.1:173-640(+)\n-AGCGAAACAAACAAATCACGTTATAGACGGTGGCAGGGCCATAAAAGGTATTCCCTCGCT\n-TTAAAAAGAAACAATGTCAAAAAGCTTTCTTTATAAACTATTGGAAGATTGAAGACATTA\n-AAGAAGAAAAGTCCTGCTTACCCTTGGACTTTTTTCAGCAGTTTTCATTGCCATGCCTAT\n-CAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAACCTGAATT\n-TCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTACTTTTCGG\n-TTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCCATTATGGG\n-TGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCATATGGAAT\n-TTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGAGCCATCTT\n-TCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGTACTTTACT\n-TGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTATGGAAAACA\n-AATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAGTTGATTTAACTGATCAAAGT\n-GAGGATTTTCACACACATTTTCAGAGTACTTGGAACGTGCCGAGCTGATTAAAAAACACC\n-GGTATTAACAAAAAATTTTATTTATGAAGCAATACGCTATTTCGTTATGAGAAACTTGAT\n-TCAATGAAACTATTATAAACCTTA\n'

diff -r b408e5a8b137 -r 0db979fead3a test-data/strand/test.fa.transdecoder.mRNA
--- a/test-data/strand/test.fa.transdecoder.mRNA Wed Jul 06 11:30:14 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r b408e5a8b137 -r 0db979fead3a test-data/top/test.fa.transdecoder.mRNA
--- a/test-data/top/test.fa.transdecoder.mRNA Wed Jul 06 11:30:14 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,266 +0,0 @@\n->CUFF.36.1|m.4 CUFF.36.1|g.4 ORF CUFF.36.1|g.4 CUFF.36.1|m.4 type:complete len:131 (+) CUFF.36.1:895-1287(+)\n-TGACTAAGTGGCAATGATGCTCCTAATGAAACCACTGATCCTCGATCATCAGCAGTAGTA\n-TCAATAGCAGCATCAGCACCGTTAGACAGCTGTTTTTCTAAACCATTCAATGATTCATCT\n-GAAAAACGTGAACCCACTTTCGAATAGTGCTTTTCAAATTTCTTTCCCGTAATTAAGGAA\n-AGTAAATCCATGTGCAGTTAGTATTGAAAAGGAAAGAATAAATAAAAGTGGGTCAAAAGT\n-AACGCCAAACAAACGAAGGTTATCGAAATATATGCGAAGGAGAGATTTATATACTAGTCA\n-AATTTAAACAGCTGAGATTGCTTTAGTCATCGCGTTGTTCCAGATCGTGAACGAAAACAC\n-CGATTCGCTCGCTAAAGTAGATACGAAATGTCCAGCAGATTTTGCTTAATTAAAACATAA\n-ATATTGATGAGCAAGAGCAGCTCGTTATAAATCAGACCTCCAAGGATTTTATCAACTACT\n-CAACTGGTTATGTGAATAATGACTCAGTTAAATATTAAATGTACTCTAAACGGTTATCAT\n-ACAATTTATTAGGAGGATTATACCAGCTAGTAGGAATTTAACCATTTCAAATTTAAACCT\n-CTTTTTTTTCGTAACTTGGGGTCGTCATAATGAATAATTCTGTTTGTCGAATTTGAAGGG\n-AAAAACACACTTGTTATCTAATTCCAAAAAAAAATAAAAAATTTTTAAAAATTAGTGGGG\n-TTTTTTTTTCACCAATGTCTAATGATGTGTGATTTAAAAAAAAACGTGTGTAACGCATTG\n-TAGTATTACTTACCTTTGCATGATTAAAAGTATATGTTGATATCGACTATTTAGAGTACT\n-GTGCGACACATTACCCTATGTTTCCCACTCTTAATCACCAAAAATTTTTTCCGAATGTCG\n-CAAGACTCAGAATCGTTCATCCGGCAACTGTTTAAGGCATTTACGGATTTTAGTACTGAC\n-GTTGAGTCACTTAGAGGATTTTTAACGCCAGATTATCGACAGCTTGTCGATGGACGTGAA\n-TTGACACTTGACGATTTTATTTCTCATGCCAAAGCACTACGTACCCATCTTCATCGGCTC\n-GACATCAACGTTCAACAAATTGTCTGTCAAGGTAACAAGGCTGCCACTGTGCATATTGCC\n-CATGCGATACGTTCCTCTGGCGAGTCCAGCAGAATCAAAGTCATTGCATTTTACAGTTTT\n-AAAGACGGGCGTATTTCTTTGATCGATGAGTTGACGTACGTTCTTGAAGGTGGTAATGCA\n-GACAGAGAGCTTGGATCAGTACAATGACTTCAATTACCTTGACACTGCATTGCCCACGTT\n-ATTCAACGTCCATCAGGAACCGGACAAATTATTCAGAGTCCTTTTGAACTACTTCATAAT\n-TTTACAAATATTCAAGTGTAATTCGTAATATAATCAGTTTTATTCATCTTCGTTGTCTAA\n-AACTTTTATGTGCTGCAATATTTGGGGAATCTCGATTTGACATAATGATCCCAGTGCC\n->CUFF.4.1|m.5 CUFF.4.1|g.5 ORF CUFF.4.1|g.5 CUFF.4.1|m.5 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+)\n-CTCTTTTTAATATTTTACCGATGAGATTGCTATTATTAGTTACGTTGCTATCTATCGTTG\n-GTTACACTAATCAGTTGCTTTCCAACTGACCTCGAAGACGCTCCAGCTGTAATCTGGGTA\n-GCCCAATTTCCTCCAGATAACACTACACAGCACTATGAATTCAGATATATCGTAAATGAA\n-TTATATAATGCTAGCAAGATGACTGCATTAATGAACCATATATATATCGATAATCCGCTT\n-ATAAGCAATTCAACTAATAACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTAT\n-AATGACGGAGAGATTTCCAGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGAT\n-GATGCTACATGGATAATCAACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAG\n-AAGCGAGACCGATACACCACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGT\n-GACACTGGAGCCAATGCTGTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGA\n-GGTGATTGGGGGGGG\n->CUFF.51.1|m.1 CUFF.51.1|g.1 ORF CUFF.51.1|g.1 CUFF.51.1|m.1 type:complete len:372 (+) CUFF.51.1:2632-3747(+)\n-CGACGTTAATAAAATATTTAACAAAGCCTTTAAAAAATTAACGATAGCTAGTCAAAGGAA\n-GCTTAACGCGTATTCAGCCTCATTAAGACAATCAGGAAGCTTTTTTTTACCATCAGCATA\n-TACCTCTAACCCTTTGATTTATTTTTATATCTCGAGATTTCGTTCGTTATTTTATAGGTC\n-GTTTCGATAAGACCTTAATACAATCTGATTTAGTGGTTGTTTAAGATTTCGGAAAAGCCT\n-TTTTTTCAAAAAAAGTTTTCCAGTTATTGTTTCATTATTTCTAATTGATTTACTGAAGAA\n-TTGTTATAACCTAAAGATGGCACTTATGTTATCCAGGATTCCACGTCGTTTTTTTTTCTT\n-ATTTTTAACGGTCGGCTTGATTGCTGGCGCGTTTCTATACTCGTTGATATATTTTGTGGA\n-CGTTGATTTGGTGTCGAAGGTTAACCAGTTGTATGATCAGCAAATTGCACCCATGCTCTC\n-CGATGCTATTGGCACTCCATCCGTTAATCACTCGTTTGAGTTGGCGCCGTTAGACTCTCA\n-TTTGGTGGCCACAAGCACTACATTCCACGAGGCGTCATACGAGTCAGAGCCTCAGCAAAA\n-TCCTGCCAGTCAAAATATTGTCTTATTACTAGTTAGTGATGGACACACTTCTTACAATAA\n-TGGAGCTAATACGTTTGAAGAAGCTATACAGAACAGAGTTGACTATAGTACCAAACAAAA\n-CTACAACTTTGAGTATGTCAATGTTACTGGCCTCCCTATTCCCGCCGTTTGGTCCAAGAT\n-GCCCGCCGTCTTACAAACTATGAAGAAATACCCCAAAGCGGAATGGATCTGGTTGTTGGA\n-TCAGGATGCAATTATTACTAATACCCATCTTTCCCTTCAAGACTCCTTTTTGAAACCTGA\n-GAACTTGCAAAAGACCTTAATTACTAATACCATCCTCACTAAACGGCCTATAAATGCTAA\n-CGGGGATTTGCGTTATACACCAAGTAATTATAGTTTAAAAGATATCGAAAATCTCATGGT\n-CATAATCTCACAGGATCACAATGGATTAAACGCAGGTAGTATCTTGTTCCGTAATTCACC\n-TGCTACTGCCTTGTTTTTGGATATTTGGACAGATCCTGTTGTTGCAGAATGTGCGAAAGC\n-CAATAATGAACAAGACATGCTTGGATATTTGATTTCTAAGCATTCACAACTTGCTTCGCT\n-GGTTGGCCTTATTCCTCAAAGAAAAATAAATGCTTTTCACGAAGGTCCGGAAAATATGGA\n-ATGGCAAAAAGGTGATTTGGTAATTCACTTTGCTGGATGTTGGGTTGAAAACCGCTGCGA\n-TGAACTATGGCAAAAGTTTTACGCCTTGATTGACTAAGTTGCTTATTCATTATATCCGTC\n-TGTTTAATTTGTTTGTGTTTTAAAAAATTTTATATATATAAACAAAGCGCCGTATAATTT\n-TCCGTCAATCTTCCTTTCTTTATCTGAATCTCTAA'..b'GGACAAGA\n-ATATATACCCCAATACTCTGTCTGTTTTACGTACTCGTGCTTCTGGTTTTGGTATCAAAA\n-TTGAATTAGACAATATCACTCCTGAACTCATTACGAAGTCTGCTAAGCATGTTTTTGGTA\n-TCTTTGTGCAATACCCAGCGGCGGATGGCTCTATTTTTGACTATGGTCATTTAGCTGCTA\n-CAGCACGCTCTTTTAATATGCACGTCGTAGCTGCCACCGATTTACTAGCTCTCACTATTT\n-TGAAATCGCCTGGGGAATGGGGTGCCGATGTTGCTGTTGGTTCCACTCAGCGCTTTGGTC\n-TGCCCATGGGCTATGGTGGCCCCCATGCCGGATTCTTTGCTTGTAGTGAAGAATTTAAAC\n-GAAAGATACCCGGTCGTCTTATTGGTCTCAGCAAAGATCGTTTAGAAAATCCCGCATACC\n-GGTTGGCTCTTCAAACAAGAGAACAACATATTCGTCGTGAAAAGGCTACAAGTAACATTT\n-GCACGGCTCAAGCTTTGTTAGCCAATATGTCTGCATTCTATGCTATTTACCATGGGCCAA\n-ATGGTCTCCAAGAAATTGCAAACCGTATTTACGCTAGTACCTCCTTCTTAAAATCTGCTT\n-TGGAATCTTCAGGATATAAAATTGTTAATAAAAGTCATTTCTTTGACACATTAACTATCG\n-AAGTTGAGTCGGCTGACAAAGTTCTTGCGAAAGCACTTGATCACGGTTACAATTTAAGAA\n-AGGTTGATGATTCACATGTTGGTCTTTCATTGGACGAGACCGTTTGCGATAAAGATATTC\n-AAGCTTTGTTTAGCATCTTTAATATAAATAAGAGTGTTGATCAGTATTATATGGAAATTG\n-CAACGTCGGAACCTAATGGAAATTCTGCTTCAACAGTCGATAATCTCAGCATTTGTTCTC\n-TTCCTGAAAACTTTAGACGAACAACCCTCTATTTACAACATCCCGTGTTTAACAGATACC\n-ATTCGGAAACTGAACTTATGCGTTATATTCATCATTTGCAGTCGAAGGATCTATCTTTAG\n-CTCATGCCATGACCCCATTGGGTTCGTGCACAATGAAGTTGAATGCTGTCACCGAAATGA\n-TGCCAATCACAAATCCATTATTTGCCAACATTCATCCATATGTTCCAGAGGAACAAGCTA\n-AAGGTTATCGTCATGTTATCGAAGATTTGCAGTTAATGTTAACGACCATCACCGGCTTTG\n-ATGCTGCATGCTTTCAACCAAATTCGGGAGCCGCTGGAGAATACACTGGCTTAAGTGTTA\n-TTCGAGCATATCAGCGGTCTATTGGTCAAGGTCATCGCAATATTTGCTTAATTCCTGTTT\n-CGGCTCACGGTACTAATCCAGCTTCAGCTGCTATGGCTGGGTTTACTGTTATTCCTGTAA\n-AATGTCTCAATAACGGTTATTTGGATATGCAAGACTTAAAAGAAAAGGCCTCTAAACACG\n-CCGACAAGTTAGCTGCCTTTATGGTAACTTATCCTAGTACTTTTGGCATTTTTGAGCCTG\n-ATGTTAAGGAAGCTTTGGAAGTAATTCACGAACATGGTGGTCAGGTTTACTTTGATGGTG\n-CTAACATGAATGCAATGGTTGGTTTATGCAAGGCTGGTGATATTGGTGCTGATGTTTGTC\n-ACTTAAATCTTCATAAGACATTTTGCATTCCTCACGGCGGTGGCGGTCCTGGTGTAGGTC\n-CTATTTGTGTAAAAAAGCATCTTGCTGATTTCCTACCATCTCATCCTGTAGTTTCATGCG\n-GCGGTAAGAATGGTATCACATCTGTTAGCTCTTCTCCTTTTGGCTCTGCTGGTATTTTAC\n-CTATCTCATGGGCATACATGAGAATGATGGGACTTGCCGGTTTGCGTGACGCTTCCAAAG\n-CCGCTCTGTTAAATGCCAATTATATGGCCAAGCGCCTGTCATCTCATTATAAACTTGTTT\n-ACACTAATAAGAACAACCTCTGTGCTCATGAGTTTATTCTAGATGCTCGCGAATTTAAAG\n-CTACTGCGGGTGTAGATGCAACTGATATAGCTAAACGTTTGCAAGATTACAGTTTCCATG\n-CACCAACTCTTTCCTGGCCTATTGCTAATACACTGATGATTGAGCCTACCGAGTCTGAGA\n-GTATGTATGAGATGGACCGCTTCTGTGATGCTTTAATTTCTATTCGACAAGAAATTCGTG\n-AAATTGAAGAAGGTCTCCAGCCTAAGGACAATAACCTGCTCGTTAATGCTCCCCACCCTC\n-AAAAGGACATTGCATCTGAGAAATGGGATCGTCCTTATACTCGAGAGCGGGCTGTCTATC\n-CTGTGCCTCTTTTAAAGGAACGGAAATTCTGGCCTAGCGTTGCTCGATTAGATGATGCGT\n-ACGGTGACAAGAACTTATTTTGTACTTGTTCCCCAGTTGTTTAGCGGTCAAAAAGAGCTC\n-ACCTGCTAGATTACTTCAACCTTTTCCCAGTTAAGTTCAACCTAATTTTTACTCCATTTG\n-GTAGTTCGTTCAACACCAATTCCCACGTTTATATATAGACCAATTTTTTACTACATCTTG\n-TTAGACAATTCTTTCCGTTATCACTTTTTCGAATTTTTTTTAATTACGTTTTAATTTTGA\n-AGGTTAGAATTATCCTTTGCTGGAACATGAGGTTTTCAACAACCTTTTTTTAATCTGATA\n-ATCTAATTTTGCTAGTCATATAATTGCGACTTTCTGATAAAAACATTACCTATACTTTAT\n-AAATATGTCGTTTTTAAATATTAACTCCTATGTCTTACTTGCATCCTTGAAATTTACGAC\n-TAGAAATTTGGTGCTTTGGATTTTCGTTACATTAAGTAAGGCCATTGAATCGATATGACA\n-CGTAAATGTTAAATTTCAAAATATTTTGGAGAGCACCATGTATAATTTAAATATACGAAT\n-TTTTTCCTTTAAATTTGTGGTTCTTTTTTAAAAAATATCAAGACGAGTACTCGATTACTC\n-GTAAGTATTCAAG\n->CUFF.9.1|m.6 CUFF.9.1|g.6 ORF CUFF.9.1|g.6 CUFF.9.1|m.6 type:complete len:156 (+) CUFF.9.1:173-640(+)\n-AGCGAAACAAACAAATCACGTTATAGACGGTGGCAGGGCCATAAAAGGTATTCCCTCGCT\n-TTAAAAAGAAACAATGTCAAAAAGCTTTCTTTATAAACTATTGGAAGATTGAAGACATTA\n-AAGAAGAAAAGTCCTGCTTACCCTTGGACTTTTTTCAGCAGTTTTCATTGCCATGCCTAT\n-CAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAACCTGAATT\n-TCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTACTTTTCGG\n-TTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCCATTATGGG\n-TGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCATATGGAAT\n-TTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGAGCCATCTT\n-TCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGTACTTTACT\n-TGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTATGGAAAACA\n-AATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAGTTGATTTAACTGATCAAAGT\n-GAGGATTTTCACACACATTTTCAGAGTACTTGGAACGTGCCGAGCTGATTAAAAAACACC\n-GGTATTAACAAAAAATTTTATTTATGAAGCAATACGCTATTTCGTTATGAGAAACTTGAT\n-TCAATGAAACTATTATAAACCTTA\n'

diff -r b408e5a8b137 -r 0db979fead3a tool_dependencies.xml
--- a/tool_dependencies.xml Wed Jul 06 11:30:14 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="transdecoder" version="2.1.0">
-      <repository changeset_revision="e564742e09aa" name="package_transdecoder_2_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>

diff -r b408e5a8b137 -r 0db979fead3a transdecoder.xml
--- a/transdecoder.xml Wed Jul 06 11:30:14 2016 -0400
+++ b/transdecoder.xml Thu Jun 01 06:04:12 2017 -0400

[

b'@@ -1,63 +1,38 @@\n-<tool id="transdecoder" name="TransDecoder" version="1.1">\n+<tool id="transdecoder" name="TransDecoder" version="3.0.1">\n <description>Find coding regions within transcripts</description>\n <requirements>\n- <requirement type="package" version="2.1.0">transdecoder</requirement>\n+ <requirement type="package" version="3.0.1">transdecoder</requirement>\n </requirements>\n \n- <stdio>\n- <exit_code range="1:" level="fatal" description="Error occurred" />\n- </stdio>\n- \n- <command><![CDATA[\n- TransDecoder.LongOrfs -t "${input}"\n- \n- #if ($min_len):\n- -m ${min_len}\n- #end if\n- \n+ <command detect_errors="exit_code"><![CDATA[\n+ TransDecoder.LongOrfs -t \'${input}\'\n+ -m ${min_len}\n ${adv.stranded}\n- \n- #if ($adv.gen_code):\n- -G ${adv.gen_code}\n+ -G ${adv.gen_code}\n+ #if str($adv.partials)\n+ -p ${adv.partials}\n #end if\n- \n &&\n- \n- TransDecoder.Predict --cpu \\${GALAXY_SLOTS:-1} -t "${input}"\n- \n- #if ($adv.retain_long_orfs):\n- --retain_long_orfs ${adv.retain_long_orfs}\n- #end if\n-\n+ TransDecoder.Predict --cpu \\${GALAXY_SLOTS:-1} -t \'${input}\'\n+ --retain_long_orfs ${adv.retain_long_orfs}\n+ ${adv.single_best_orf}\n #if str( $training_sect.training.training_selector ) == "training_top":\n- #if ($training_sect.training.top_longest):\n- -T ${training_sect.training.top_longest}\n- #end if\n+ -T ${training_sect.training.top_longest}\n #else\n- #if ($training_sect.training.train):\n- --train ${training_sect.training.train}\n- #end if\n+ --train \'${training_sect.training.train}\'\n #end if\n- \n &&\n-\n- out_prefix=`basename "${input}"`\n-\n- mv `basename "${input}"`.transdecoder.pep transcript.transdecoder.pep &&\n- mv `basename "${input}"`.transdecoder.cds transcript.transdecoder.cds &&\n- mv `basename "${input}"`.transdecoder.bed transcript.transdecoder.bed &&\n- mv `basename "${input}"`.transdecoder.gff3 transcript.transdecoder.gff3 &&\n- mv `basename "${input}"`.transdecoder.mRNA transcript.transdecoder.mRNA\n+ mv `basename \'${input}\'`.transdecoder.pep \'$transdecoder_pep\' &&\n+ mv `basename \'${input}\'`.transdecoder.cds \'$transdecoder_cds\' &&\n+ mv `basename \'${input}\'`.transdecoder.bed \'$transdecoder_bed\' &&\n+ mv `basename \'${input}\'`.transdecoder.gff3 \'$transdecoder_gff3\'\n ]]></command>\n- \n <inputs>\n- <param format="fasta" name="input" type="data" label="Transcripts"/>\n- \n- <param name="min_len" size="5" type="integer" optional=\'true\' value="100" label="Minimum protein length (default: 100aa)"/>\n- \n+ <param name="input" argument="-t" type="data" format="fasta" label="Transcripts" />\n+ <param name="min_len" argument="-m" type="integer" value="100" label="Minimum protein length" />\n <section name="adv" title="Advanced Options" expanded="False">\n- <param name="stranded" type="boolean" checked="false" truevalue="-S" falsevalue="" label="Strand-specific" help="Only analyzes top strand"/>\n- <param name="gen_code" type="select" label="Genetic code">\n+ <param name="stranded" argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Strand-specific" help="Only analyzes top strand" />\n+ <param name="gen_code" argument="-G" type="select" label="Genetic code">\n <option value="universal" selected="True">universal</option>\n <option value="Euplotes">Euplotes</option>\n <option value="Tetrahymena">Tetrahymena</option>\n@@ -75,10 +50,10 @@\n <option value="Mitochondrial-Euascomycetes">Mitochondrial-Euascomycetes</option>\n <option value="Mit'..b'bed\' format=\'bed\' label="${tool.name} on ${on_string}: bed" from_work_dir="transcript.transdecoder.bed"/>\n- <data name=\'transdecoder_gff3\' format=\'gff3\' label="${tool.name} on ${on_string}: gff3" from_work_dir="transcript.transdecoder.gff3"/>\n- <data name=\'transdecoder_mRNA\' format=\'fasta\' label="${tool.name} on ${on_string}: mRNA" from_work_dir="transcript.transdecoder.mRNA"/>\n+ <data name="transdecoder_pep" format="fasta" label="${tool.name} on ${on_string}: pep" />\n+ <data name="transdecoder_cds" format="fasta" label="${tool.name} on ${on_string}: cds" />\n+ <data name="transdecoder_bed" format="bed" label="${tool.name} on ${on_string}: bed" />\n+ <data name="transdecoder_gff3" format="gff3" label="${tool.name} on ${on_string}: gff3" />\n </outputs>\n-\n-\n <tests>\n <test>\n <param name="input" value="test.fa"/>\n <output name="transdecoder_gff3" file="raw/test.fa.transdecoder.gff3" compare="sim_size" />\n <output name="transdecoder_bed" file="raw/test.fa.transdecoder.bed" compare="sim_size" />\n <output name="transdecoder_cds" file="raw/test.fa.transdecoder.cds" compare="sim_size" />\n- <output name="transdecoder_mRNA" file="raw/test.fa.transdecoder.mRNA" compare="sim_size" />\n <output name="transdecoder_pep" file="raw/test.fa.transdecoder.pep" compare="sim_size" />\n </test>\n <test>\n@@ -122,7 +90,6 @@\n <output name="transdecoder_gff3" file="top/test.fa.transdecoder.gff3" compare="sim_size" />\n <output name="transdecoder_bed" file="top/test.fa.transdecoder.bed" compare="sim_size" />\n <output name="transdecoder_cds" file="top/test.fa.transdecoder.cds" compare="sim_size" />\n- <output name="transdecoder_mRNA" file="top/test.fa.transdecoder.mRNA" compare="sim_size" />\n <output name="transdecoder_pep" file="top/test.fa.transdecoder.pep" compare="sim_size" />\n </test>\n <test>\n@@ -131,7 +98,6 @@\n <output name="transdecoder_gff3" file="gencode/test.fa.transdecoder.gff3" compare="sim_size" />\n <output name="transdecoder_bed" file="gencode/test.fa.transdecoder.bed" compare="sim_size" />\n <output name="transdecoder_cds" file="gencode/test.fa.transdecoder.cds" compare="sim_size" />\n- <output name="transdecoder_mRNA" file="gencode/test.fa.transdecoder.mRNA" compare="sim_size" />\n <output name="transdecoder_pep" file="gencode/test.fa.transdecoder.pep" compare="sim_size" />\n </test>\n <test>\n@@ -140,12 +106,10 @@\n <output name="transdecoder_gff3" file="strand/test.fa.transdecoder.gff3" compare="sim_size" />\n <output name="transdecoder_bed" file="strand/test.fa.transdecoder.bed" compare="sim_size" />\n <output name="transdecoder_cds" file="strand/test.fa.transdecoder.cds" compare="sim_size" />\n- <output name="transdecoder_mRNA" file="strand/test.fa.transdecoder.mRNA" compare="sim_size" />\n <output name="transdecoder_pep" file="strand/test.fa.transdecoder.pep" compare="sim_size" />\n </test>\n </tests>\n <help>\n-\n **What it does**\n \n TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.\n@@ -163,9 +127,8 @@\n - optional the putative peptide has a match to a Pfam domain above the noise cutoff score.\n \n The software is primarily maintained by Brian Haas at the Broad Institute and Alexie Papanicolaou at the Commonwealth Scientific and Industrial Research Organisation (CSIRO). It is integrated into other related software such as Trinity, PASA, EVidenceModeler, and Trinotate.\n-\n </help>\n- <citations>\n+ <citations>\n <citation type="doi">10.1038/nprot.2013.084</citation>\n </citations>\n </tool>\n'