| Next changeset 1:d763e35fef0b (2015-10-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636 |
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added:
macros.xml test-data/sequence.fasta test-data/sequence.gff3 test-data/sequence.gff3.out tool_dependencies.xml transtermhp.py transtermhp.xml |
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| diff -r 000000000000 -r c28817831a24 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Oct 09 09:22:42 2015 -0400 |
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| @@ -0,0 +1,25 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.09">transtermhp</requirement> + <requirement type="package" version="1.65">biopython</requirement> + <requirement type="package" version="0.6.2">bcbiogff</requirement> + <yield/> + </requirements> + </xml> + <token name="@WRAPPER_VERSION@">2.09</token> + <xml name="stdio"> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:"/> + <exit_code range=":-1"/> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:"/> + <regex match="Exception:"/> + </stdio> + </xml> + <!--<xml name="in_fq">--> + <!--<param name="in_file" type="data" format="fastq" label="Input FASTQ file"/>--> + <!--</xml>--> +</macros> |
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| diff -r 000000000000 -r c28817831a24 test-data/sequence.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sequence.fasta Fri Oct 09 09:22:42 2015 -0400 |
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| b'@@ -0,0 +1,574 @@\n+>KT001911\n+CCAGCTAAGAAAAGATTTAATATGATGTGCAAGTAAGGTGTAAATTGGCTGCGGAAACAGTCAACCTTCT\n+TCCATACAAGAGTTGAGTGCAAACAACTATTCATTTTGGTTATGTTATAGTCCTTGAAACAAAATACAGT\n+GCTAGGCTGCTTTCTTTATGAAGGTAGCTTTTTTTATTTGCAAAAATATATAATTGGTTTACATGTTGAA\n+CGAAAGGAGCTTAGAACATGGCTAGATTAACACCTAAGCAACAAATGTTTGTTAAAGAGTATCTAATTGA\n+CTTGAACGCAACACAAGCGGCTTTACGTGCTGGCTATAGTGCAAAGACTGCTAAACAAACAGGCACAGAG\n+AACCTATCTAAACCTATCATTCAAGCTGAGATACAGAAGCACATGAACAATAGGGCTGAGAAGATTGACG\n+TTAGCGCTGACCGCATTTTACAAGAGTTGGCTGCTATTGCCTTTCATGATGTAAATGAGGTTGTGTATGT\n+CGATACAAGGGAGTATGTGAGCGGCTGGAAGATTACTCAAAAAGAAACAGATGAACAACCGGAAATAAAA\n+GAACCTATGTACAGCACCGCGCAAATGGTTGTTGTAAAAGATTTATCGGAGCTTACGCCGCTGCAGCGCA\n+AAAGTATTGCCGCTATTAAGCAAGGTAAAGAAGGTATTGAAATAAAGTTTCATGACAAGATTAAGGCTGC\n+TGAATTACTCGGCAAACATATGAAACTATTCGCTGATAAGATTGAACACAGCGGAGAAATTACTCATAAT\n+ACAGTAGATTTGAGCGGGCTTTCTACGGAGGAGCTGAGAAAACTTGCTAAAATTGAGTGAATCACAACGA\n+ATTGCTGTTGCTATCGAAGCACAGAAGGAACTTGCACGCCGTAATTACGGTGACTATGTTACTTATGTTC\n+ATCAGGGGCGCTATGTACACGCAAGGCACACGCTCTTTATTACCGATATTCTGCAGCGTGCCATTGATAA\n+CAAAAAGAAAATGCGATCAGGTGAAATAGAAACAGAAAACCAATACATCATGATTAATATGCCGCCGCGT\n+CATGGTAAGTCAATGACAGCTACGGAAACATACCCTAGCTATTATCTTGGTCACTTTCCAGAGGATAGAG\n+TTATAGAGATAAGCTACAATGATACCTTTGCAAAGAAGTTCGGTAAGAAGAATAAAGAGAAGGTTAGGCA\n+GTTCGGCGTTGATTTATTCGGCGTGAATGTTTCTAAGCGAGCTTCTGCCACAGATACATGGTATTTAGAG\n+AATGAAATAGGCGGTATGCTTTCGCGTGGTGCTCTTGCTGGTATCACTGGCGAAGGGGCAGACCTCATGT\n+TAATTGATGACCCAATAAAGAACAGGGAAGAAGCTGACAGCGAAACGCACAGGGAAAAACTTTGGAATGA\n+ATGGGTAGATAGCTTTTCTTCTCGTTTACACCCCGGCGCTATTGTCATTATCATTCTTACACGTTGGCAT\n+GAAGATGACTTACAAGGGCGCTTACTATCTAAAGAATATGGTGAACCGCTGCCCTGGCAAGTGTACAATT\n+TCCCGCTAGAAGCTGACGAGAAACACGTTAACGAAGAAGGCAACCAGCTCAATAGAGAAATAGGCGAACC\n+ACTTTGGCCCGAACGTTACGGCAAGAAGTTCATTGAACAACGTAAGCTCTACCCTTCTTCTTTTAATTCA\n+CTTTATCAAGGTAGACCAACAGCGGCAGAAGGTAATATGCTTAAAAGGCATTGGTGGAACTTCTATGATG\n+AGTACCCTATTGTCGCTCAGGAACTTATTTCGGTTGATGCCACGTTTAAAGATAAAGATGATAGCGATTA\n+TGTTTCTATTCAAGTGTGGGGCAAGGTTGGAATGGATATGTACCTAAAAGACCGCATTAAGGCGCGTATG\n+AATTTCCCCGCTACTTTAAAAGCGGTGCGTAACATGATTAAGCGTCACCCTGCAGCAGTTATCCGCTTAA\n+TAGAGGATAAAGCAAACGGCACAGCTATCATATCTATGCTACACAGGGAAATAGGCGGTATAATTGCAGT\n+AAATCCGCAAGGCGGTAAAGTCGCACGCGTTCAAGCTGTTTCTCCTTTTATTGAAAGTGGTAACGTATGG\n+CTACCAAGACACGAGCCATTTACACAGGAAATCATAGAAGAAGCTGCAGCATTTCCGAATGGGGCGCATG\n+ATGATGATGTGGATTCGATGTCTCAGGCGTTAAATAGATTCATCTATCACACTGGCGAACTACCGGAGCC\n+GGAAAAACCACCATTGCCGCAAGCGTTCCAAACTAATCACGATGAGGAAGGGGATTTTTTAACATGGTAA\n+CTGAAATATTATGTGGAGTCAGTGGGGTTGCTATTGGTTATATTGGCTATTTAATTGCGACACTTAAAGC\n+TGCAAAGAAAGAGAATCAACATGACCGCCTATACGACAATTTGCACACAAAATATACTAATTTAGTTAGT\n+GAAGATGTGCAATTGCAAGCGGATTATAAGCAATTGAAGGCAGACTTTCAACAATTAGCGGAGGAACATG\n+CAGCAAGAAAAGAAGCTAACTCTAAATTAGCTGCAGGCAACAACGCTATTGCTAAGGAGTACCACGATTT\n+AAAAGCGAAATACGAAACGTTAAAAGAGAATCATGCGCCGTTTGCTGCTTTAAATCCATTTGAAGCACAA\n+GCTATGCACGCTATGGCTAGTCAATCGGTAGTAGACGAATGGTTAAACGGAGAAAAGGAGGTTAAATAAT\n+GGCTAAACAACAACAGCAAGCCGCTGCAACAGGTAGCGAACCGAAAACAGTCATGCCGCCGGAACAAATG\n+GAGCTCATTTCTCAACGTGCTCAAAAGGTTGAGAAGGAGTATAAACAGTCACTTGACTATAAGCGGTCAC\n+AAAACTTCCTTACATCATGGGCTACATACGAGAGATTCAAGGCAGGGGACCAATGGCCCGCAGTAACAGA\n+ACGTACAAAGATGTTACCGCGTCCAGTGTTTAATATCATTGAACAAATTGTAGGGCATAAAGTTGCAACG\n+ATCATGAACGAAAATATTAAAATGGTCTTTTCTGCTTTAGATGTTGACGAACCGGACCAAGATAACCCGG\n+AGCTTCAAGGGCAAGACATTGAACAGTGGGAAGGCGCTGACTTATTCAGTAAATACAGTGATAGCGTATG\n+GGAGCACATTAAACAAGATATGCTCAACGAAGAAATGTTAGAGAATGCCGCCGCTGTTGGTAGTGGCTTC\n+ATTCACTACTATTGGGACCCTAATGTAAAAGGCGGTAACAAGCTGAAATACAACGGTGACATTAAAGGCG\n+AAGTAATTGACGCGGTTAATTTCTTCCCTGGCAATCCGCAAGTTGCTGACGTTCAGAAGCAACCATATAT\n+CATTATCACGAGCCGCGAGCTTGTAAGTGATGTGAAGAACGCTGCTATTAATAACGGTTTGCCGCCTGAG\n+TATGTCGATATGATTAAAGAGGACAAAGAAACGCAAGACCAGGCATACGATATGGCACAGAATGAACAGG\n+ACGGAGATAGCAAGATTACTGTATTAACCCGCTATTATAAGAAGAATGGTGAAGTACATTTTGTTAAAGT\n+TGCAGCAGGCGTATTAATTAAAGATGAAACGCCTATGGGCTTTGAACGTTACCCAATTGTTATGATGAAC\n+TGGAAGCGCCGTAAGAAATCTATTTTCGGTGTTGGAGATATTGAGAGCTTAATTCCCAATCAAAAAGCTA\n+TTAACTTCTTAATGGCTATGCAGCTTCTTTCTGCTCAATTAACAGGTTGGCCGAAGATGGTCGTTAACCG\n+CTCATATGTTAAGCAGCGTATTAAGAATGAGCCGGGCGAAATCATTTATACAGATGCACCACCGGATAAA\n+CCGAACAGC'..b'ACAAATGGTTAAAAGCCATTATGAGGGGGAGTATTCACGATGTTGAATAGAG\n+AAGAAAAGAAAAGTGCTCGAAGTGCTGTTAGTGGGTTAATGAATGTAGCTTGTGCAAGATGTACAACGCC\n+TAACGAATGTGAAGGCTGCCCAATTCAAGCGGCTATGCAATCAATGTATTGCCTTATCGAAGGAAAAGAA\n+AGCTGGAAGAAGGCAACAGCAGGCATTACAGAACGCCGCTATCGTAAGTTACGCGCCCAGGGCTTCCATG\n+ATGCTGATATTGCGGAGATATACGGCATTACACCTAAGCAGCTCCTAGACTTCAAGCGCCGCGAAGGAAT\n+GATAGCAACACACCTGACTGATGAGGACATAAGAGAATTACGCCGGTTACGCAATGAGGAAAAGTGGAAG\n+TATCAAGATATTGCTGAAAAATACGGCATTACGCCAACATACGCAAGTGAAGTAGCTCGCGGCAAACGAT\n+TCCCGGAGGTGGTTTAAATGTGCGAATTAAAAAGCACTCTGTCATTAGTTGAAATGGCAGCTAAAGAAAA\n+TCCAGCAGTTTTAAAAGGTATACACGATCTTTTAAACAAATACGAAAACGCCGGTGCTACCAACACCAGC\n+GCAAAGAATAAACACTCTGTCAAAAGTCATATTCAATTTAATGATACCCATAAAAGCCTAATTGTATTCT\n+GCTTTAATTGCAATCTTACAAATGAACTAACCCTAAAGAACGTGATTTCTTACAAATGCCGTCATTGCGA\n+TTGGGAAAACCGCCTAAGCTACATGCAAGCTCGGTACATGCGCGAGCTATGAAAAAGTTAATCAACGGTG\n+AACACCTCACCATAGACGAAGCATGGGCAAAACATAAGGGGCTATGTTGGAAATACGTTAGATGTAATAT\n+GGAACGTGCCAAGCGTATGAGCTACACAAAAGCTGATTTAATACAAACGGCTGCTATGGCATTTACCCAG\n+GCATACAACGGTTTTGATGAAAATGCAGGGGTAAAGTTTAGCACTTATGCCGTTCCTGTCATATTCGGTG\n+TAATGGATAACGCTTTCTCACGAAACAATGCGGGCTTACATTACTCAGAACCAGTTAAAAGCCTTGCTTA\n+CAGGTATTTAAAAGGCAAAAGCAAGGAAGAAAGAGAAATATCACAGTTAGATGACATCATGAATAGCCTT\n+CAGATTGATTATTCTCGCGCGTATGACGTTTTTCAGTTCATTCACAATGAATTACTCTTTTCAATGGATT\n+TTCCCGTTACAATCGAAAATACGACAGGTTCCGGCGAAATGGTTGGAAGTAATCATTGGGACATCATCGG\n+GCAAGAAGCTGATTACTCATCAATTTTTATCAATGAGTTAAAAAGTCATTGTACTGAATTAGAAAATCAG\n+GTTATTGATTTGATATTCATAGGGGTTGAGCGCCGAGATATGCCCGAAATACTCGGCGTAAAGCCCACCA\n+ATATCTTTTCTAGGGTGCAACGTATTAAACGCAGAATACGAGAAAAGGGGCTTTTACATGATGGACAACC\n+ACCTGCAATTACTAAATGATATGCTACACAATTTAAAATATGACACGCTTTATGCAGATTTACAGGACTA\n+TGTTCCAGCTCTGGAAGCTATGGTGAAGGTTTATAAGCATAATGCTGAGGTACTTGAAGAAAAACGCGCC\n+TTAGAAAACGAAATGCGCGAAGTAAAAAAGAGCTACATGCAGACCATTGAGAAATTGAAGTCCTATAAGA\n+AGCGCAACCAAGAACAAAAGTTGCTGCTTGGTCAAATAAAATCTCTTGCTGCAGGAGGTAAACCAATTGA\n+AAACTAAAAAGCAACGATGGAGAAAAACAAAATTTTCAACTTGGAAATGGTCTTGTGAAGGTTGCGGAAA\n+AAGCACACATACAAACGGCTGCAAGTTTCCTAAAGGTTGGCATTACGGCGGGTATGGCGTTGTTTTTGTC\n+ACTTGCAAGGAGTGTGGACCATTTGAAGAAAATTGATTTCGGTTTCAATCCAGTAGCAAAACCCAATTAC\n+AAGCGCTCTAAGCCCACAGCAAAGGAGCGCGGTAAGTTTAGTAGTGAAACTATCTTAAACATTCATATAC\n+GCGATAACGGCAAATGTGTGTGTTGTGGCAGCGGTAGAGTTGAAGCAGTACCGCACCACGTTATTTTTCG\n+CAGTCAAGGCGGCACAGGTACAGAAGATAACGGCGTGTTGGTTTGTTCTCCTTGTCATCTATGGGCACAT\n+GGTAGAGCAGATGGGCCAAACGGCGAACCATTCAACGAGGGGCGAAAGTGGTTTGAAAATTATAGGGAGG\n+AAAATTTACTATGATGATCTATTTTGAACAGCTAAATGTTGTCACTGTTGCCTATATGCAAGCATGTATG\n+GAAATATGGAAGGGGCGATTTACTCATGATTGAATATGAAATGACTGTACAGGCGGATAGAATAGCGCCT\n+TATAAGTTTAGTTTTAAATCAAATGATGCCAATTTATTAAAAGCTGCTGAACGTTTCGAGCGTCATATTG\n+CAGAACATGACTTCATTTGCTCGGATAACATGGAATTTTTACGTACAAGCACTATAACAAGCTTTAAGCC\n+TAAGCAAAAAACGCCTATTGTTGACGCAAAAGCGAAGGCAACGGAAGTAATAGAGAACTATTTAAAACAT\n+AATGGTCCTGCTATTACAGTAGATTCAGTTATTTACATGTACAAAAGGGATTATTTAAACGGCGGGCGCG\n+ATATTAACCCAAGTATAAAGGCTGTTATTGAATCAAACATCAACGAAATTAAATTACTTTCCCAGGAGGA\n+ATATAAAAATGATTAATCAATCAATCGTAGTTGGACGCTTAACAAAAACGCCGGAGCTTCGTTATACTCC\n+AAGCGGCGCAGCAGTAACAAACTTCACAGTAGCATGTAACAAGCCTAAGAAAGATGGTAAAGACCAGGGC\n+GCAGACTTCATCAATTGTGTTGCATGGAATAAACAAGCGGAGAATCTTTGCAACTATCAAACAAAAGGTG\n+CTCTTATCGGTGTAACAGGGCGTACAACTACACGCAGCTATGAAGATAACAGCGGCAAAAAGGTATATGT\n+ACAAGAAATACTAGCTCAGAGCATTCAGTTTCTCGAATTTAGGGATAATAACGGCGGGAATAGTAATACA\n+TCTAATCAGGGTACGGCGTTCGATGAGGGCGAAACAATGGATATTCAAGATGATGATTTGCCGTTTTGAT\n+AAAAGGCTTACTATGGGGCGTGCTTCTTAGCATTCCCCTATGGCTTGCTATATTGGGATATATAAAACTA\n+TTTAAGGGGCTGTTGGAATGAATTTAAAAGAATTATTTGAGATACAAGCGGGTTTAGATGCAGAAATATT\n+AAAGAATCACCCTATTCAACCAGGAGAGGACCGTTTAGAAAAGAAACATGCTGCTTTATTGGTGGAGCTA\n+GGGGAAATGTTCAACGAGTGGAGAGCATTTAAGTTTTGGAGTCACGATAAAGAACCGCGTATGGCTGTAA\n+AATGTCCTGAGTGTGAAGGAGCTGCAGCGCGTCAAGCTTCTGACGGTAGTTATGTAGAGTGTGGCACATG\n+TGATGGAGCTGGAACAATTGATAAAGTATTAAAAGAGCTAGTGGACTGCTTACACTTTGTTTTAAGTATT\n+GGGTTAGAACATGAATTTGATACAAAATTAAATATGGTCATTGAACCAATTTTATTTAGCCGCTCGGACG\n+ATGGTAATAATATCATTGCTCAGTTCATTGAATTATTAAAAGTTGAGTGGGAGCTAGTAGGTAGACACTA\n+TAAAGAAGGTTTGGAGCTGTTTATAGGCTTTTGTGAAATGCTAGGCTATACATGGGAGCAAGTAAGAGAA\n+GCATACCTCATTAAGAACCAAGAAAATCATTACAGACAAATGAATGGCTATTGA\n+\n' |
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| diff -r 000000000000 -r c28817831a24 test-data/sequence.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sequence.gff3 Fri Oct 09 09:22:42 2015 -0400 |
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| @@ -0,0 +1,56 @@ +##gff-version 3 +##sequence-region KT001911 1 40024 +# conversion-by bp_genbank2gff3.pl +# organism Bacillus phage Pavlov +# Note Bacillus phage Pavlov, complete genome. +# date 10-SEP-2015 +KT001911 GenBank gene 215 830 . + 1 ID=CPT_Pavlov1;Name=CPT_Pavlov1 +KT001911 GenBank gene 799 2310 . + 1 ID=CPT_Pavlov2;Name=CPT_Pavlov2 +KT001911 GenBank gene 2290 2729 . + 1 ID=CPT_Pavlov3;Name=CPT_Pavlov3 +KT001911 GenBank gene 2716 4636 . + 1 ID=CPT_Pavlov4;Name=CPT_Pavlov4 +KT001911 GenBank gene 4722 5527 . + 1 ID=CPT_Pavlov5;Name=CPT_Pavlov5 +KT001911 GenBank gene 5535 6512 . + 1 ID=CPT_Pavlov6;Name=CPT_Pavlov6 +KT001911 GenBank gene 6565 6926 . + 1 ID=CPT_Pavlov7;Name=CPT_Pavlov7 +KT001911 GenBank gene 6929 7366 . + 1 ID=CPT_Pavlov8;Name=CPT_Pavlov8 +KT001911 GenBank gene 7368 7758 . + 1 ID=CPT_Pavlov9;Name=CPT_Pavlov9 +KT001911 GenBank gene 7777 10001 . + 1 ID=CPT_Pavlov10;Name=CPT_Pavlov10 +KT001911 GenBank gene 10011 10422 . + 1 ID=CPT_Pavlov11;Name=CPT_Pavlov11 +KT001911 GenBank gene 10421 11010 . + 1 ID=CPT_Pavlov12;Name=CPT_Pavlov12 +KT001911 GenBank gene 11009 12713 . + 1 ID=CPT_Pavlov13;Name=CPT_Pavlov13 +KT001911 GenBank gene 12712 14596 . + 1 ID=CPT_Pavlov14;Name=CPT_Pavlov14 +KT001911 GenBank gene 14599 16395 . + 1 ID=CPT_Pavlov15;Name=CPT_Pavlov15 +KT001911 GenBank gene 16396 17290 . + 1 ID=CPT_Pavlov16;Name=CPT_Pavlov16 +KT001911 GenBank gene 17290 17641 . + 1 ID=CPT_Pavlov17;Name=CPT_Pavlov17 +KT001911 GenBank gene 17629 18895 . + 1 ID=CPT_Pavlov18;Name=CPT_Pavlov18 +KT001911 GenBank gene 18940 19800 . + 1 ID=CPT_Pavlov19;Name=CPT_Pavlov19 +KT001911 GenBank gene 19793 24845 . + 1 ID=CPT_Pavlov20;Name=CPT_Pavlov20 +KT001911 GenBank gene 24844 25080 . + 1 ID=CPT_Pavlov21;Name=CPT_Pavlov21 +KT001911 GenBank gene 25114 25539 . + 1 ID=CPT_Pavlov22;Name=CPT_Pavlov22 +KT001911 GenBank gene 25523 25718 . + 1 ID=CPT_Pavlov23;Name=CPT_Pavlov23 +KT001911 GenBank gene 25703 26446 . + 1 ID=CPT_Pavlov24;Name=CPT_Pavlov24 +KT001911 GenBank gene 26644 26825 . + 1 ID=CPT_Pavlov25;Name=CPT_Pavlov25 +KT001911 GenBank gene 27050 28228 . + 1 ID=CPT_Pavlov26;Name=CPT_Pavlov26 +KT001911 GenBank gene 28223 28787 . + 1 ID=CPT_Pavlov27;Name=CPT_Pavlov27 +KT001911 GenBank gene 28881 29099 . + 1 ID=CPT_Pavlov28;Name=CPT_Pavlov28 +KT001911 GenBank gene 29075 29331 . + 1 ID=CPT_Pavlov29;Name=CPT_Pavlov29 +KT001911 GenBank gene 29316 29501 . + 1 ID=CPT_Pavlov30;Name=CPT_Pavlov30 +KT001911 GenBank gene 29529 31498 . + 1 ID=CPT_Pavlov31;Name=CPT_Pavlov31 +KT001911 GenBank gene 31483 31671 . + 1 ID=CPT_Pavlov32;Name=CPT_Pavlov32 +KT001911 GenBank gene 31651 32599 . + 1 ID=CPT_Pavlov33;Name=CPT_Pavlov33 +KT001911 GenBank gene 32585 33297 . + 1 ID=CPT_Pavlov34;Name=CPT_Pavlov34 +KT001911 GenBank gene 33297 33424 . + 1 ID=CPT_Pavlov35;Name=CPT_Pavlov35 +KT001911 GenBank gene 33408 33852 . + 1 ID=CPT_Pavlov36;Name=CPT_Pavlov36 +KT001911 GenBank gene 33982 34211 . + 1 ID=CPT_Pavlov37;Name=CPT_Pavlov37 +KT001911 GenBank gene 34201 35052 . + 1 ID=CPT_Pavlov38;Name=CPT_Pavlov38 +KT001911 GenBank gene 35078 35815 . + 1 ID=CPT_Pavlov39;Name=CPT_Pavlov39 +KT001911 GenBank gene 35820 35990 . + 1 ID=CPT_Pavlov40;Name=CPT_Pavlov40 +KT001911 GenBank gene 35980 36188 . + 1 ID=CPT_Pavlov41;Name=CPT_Pavlov41 +KT001911 GenBank gene 36163 36627 . + 1 ID=CPT_Pavlov42;Name=CPT_Pavlov42 +KT001911 GenBank gene 36615 36942 . + 1 ID=CPT_Pavlov43;Name=CPT_Pavlov43 +KT001911 GenBank gene 36923 37679 . + 1 ID=CPT_Pavlov44;Name=CPT_Pavlov44 +KT001911 GenBank gene 37637 37947 . + 1 ID=CPT_Pavlov45;Name=CPT_Pavlov45 +KT001911 GenBank gene 37983 38444 . + 1 ID=CPT_Pavlov46;Name=CPT_Pavlov46 +KT001911 GenBank gene 38426 38533 . + 1 ID=CPT_Pavlov47;Name=CPT_Pavlov47 +KT001911 GenBank gene 38512 38936 . + 1 ID=CPT_Pavlov48;Name=CPT_Pavlov48 +KT001911 GenBank gene 38914 39339 . + 1 ID=CPT_Pavlov49;Name=CPT_Pavlov49 +KT001911 GenBank gene 39416 40024 . + 1 ID=CPT_Pavlov50;Name=CPT_Pavlov50 |
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| diff -r 000000000000 -r c28817831a24 test-data/sequence.gff3.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sequence.gff3.out Fri Oct 09 09:22:42 2015 -0400 |
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| @@ -0,0 +1,10 @@ +##gff-version 3 +##sequence-region KT001911 1 40024 +KT001911 annotation remark 1 40024 . . . gff-version=3;sequence-region=%28%27KT001911%27%2C 0%2C 40024%29 +KT001911 TransTermHP_2.09 terminator 6521 6544 100 + . ID=TERM 1 +KT001911 TransTermHP_2.09 terminator 7749 7766 83 + . ID=TERM 2 +KT001911 TransTermHP_2.09 terminator 25063 25096 80 + . ID=TERM 3 +KT001911 TransTermHP_2.09 terminator 25071 25088 100 + . ID=TERM 4 +KT001911 TransTermHP_2.09 terminator 26456 26474 100 + . ID=TERM 5 +KT001911 TransTermHP_2.09 terminator 28782 28801 100 + . ID=TERM 6 +KT001911 TransTermHP_2.09 terminator 33846 33869 93 + . ID=TERM 7 |
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| diff -r 000000000000 -r c28817831a24 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Oct 09 09:22:42 2015 -0400 |
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| @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="transtermhp" version="2.09"> + <repository changeset_revision="0a21f73e2f15" name="package_transtermhp_2_09" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="biopython" version="1.65"> + <repository changeset_revision="dc595937617c" name="package_biopython_1_65" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bcbiogff" version="0.6.2"> + <repository changeset_revision="8adfe232049d" name="package_python_2_7_bcbiogff_0_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
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| diff -r 000000000000 -r c28817831a24 transtermhp.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transtermhp.py Fri Oct 09 09:22:42 2015 -0400 |
| [ |
| @@ -0,0 +1,70 @@ +#!/usr/bin/env python +import sys +import re +import subprocess +from Bio import SeqIO +from BCBio import GFF +from Bio.SeqFeature import SeqFeature, FeatureLocation + + +def main(expterm, fasta, gff3): + with open(fasta, 'r') as handle: + seq_dict = SeqIO.to_dict(SeqIO.parse(handle, "fasta")) + + # Build coords file + with open(gff3, 'r') as handle: + for rec in GFF.parse(handle, base_dict=seq_dict): + with open('tmp.coords', 'w') as coords: + for feat in rec.features: + if feat.type == 'gene': + coords.write('\t'.join([ + feat.id, + str(feat.location.start + 1), + str(feat.location.end), + rec.id, + ]) + '\n') + with open('tmp.fasta', 'w') as fasta_handle: + SeqIO.write(rec, fasta_handle, 'fasta') + + cmd = ['transterm', '-p', expterm, fasta, 'tmp.coords'] + output = subprocess.check_output(cmd) + # TERM 1 4342 - 4366 + F 93 -11.5 -3.22878 | opp_overlap 4342, overlap 4340 4357 + ttre = re.compile( + '^ (?P<name>.*) (?P<start>\d+) - (?P<end>\d+)\s+' + '(?P<strand>[-+])\s+(?P<loc>[GFRTHNgfr]+)\s+' + '(?P<conf>\d+)\s+(?P<hp>[0-9.-]+)\s+(?P<tail>[0-9.-]+)' + ) + + rec.features = [] + batches = output.split('SEQUENCE ') + for batch in batches[1:]: + batch_lines = batch.split('\n') + # Strip the header + interesting = batch_lines[2:] + unformatted = [x for x in interesting if x.startswith(' ')][0::2] + for terminator in unformatted: + m = ttre.match(terminator) + if m: + start = int(m.group('start')) - 1 + end = int(m.group('end')) + if m.group('strand') == '+': + strand = 1 + else: + strand = 0 + + feature = SeqFeature( + FeatureLocation(start, end), + type="terminator", + strand=strand, + qualifiers={ + "source": "TransTermHP_2.09", + "score": m.group('conf'), + "ID": m.group('name'), + } + ) + rec.features.append(feature) + yield rec + +if __name__ == '__main__': + for record in main(*sys.argv[1:4]): + GFF.write([record], sys.stdout) |
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| diff -r 000000000000 -r c28817831a24 transtermhp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transtermhp.xml Fri Oct 09 09:22:42 2015 -0400 |
| [ |
| @@ -0,0 +1,76 @@ +<?xml version="1.0"?> +<tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.0"> + <description>finds rho-independent transcription terminators in bacterial genomes</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command><![CDATA[ +#if $reference_genome.source == 'history': + ln -s $reference_genome.genome_fasta genomeref.fa && +#end if + +python $__tool_directory__/transtermhp.py \$TRANSTERM_EXPTERM_DAT + +#if $reference_genome.source == 'cached': + "${reference_genome.fasta_indexes.fields.path}" +#elif $reference_genome.source == 'history': + genomeref.fa +#end if + +$input_gff3 + +> $output]]></command> + <inputs> + <conditional name="reference_genome"> + <param name="source" type="select" label="Reference Genome"> + <option value="cached">Locally Cached</option> + <option value="history">From History</option> + </param> + <when value="cached"> + <param name="fasta_indexes" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"/> + </param> + </when> + <when value="history"> + <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> + </when> + </conditional> + <param name="input_gff3" type="data" format="gff3" label="GFF3 formatted Gene Calls"/> + + <!-- Currently we do not support ANY of the command line options for + TransTermHP due to the following statement: + + As mentioned above, if you change any of the basic scoring + function and search parameters and are using the version 2.0 + confidence scheme (recommended) then you have to recompute + the values in the expterm.dat file. If you have python + installed this is easy (though perhaps time consuming). + + ref: http://manpages.ubuntu.com/manpages/precise/man1/transterm.1.html + + This is a TODO item that would be nice to get around to eventually + (perhaps when a user demands it.) + --> + </inputs> + <outputs> + <data format="gff3" name="output"/> + </outputs> + <tests> + <test> + <param name="source" value="history" /> + <param name="genome_fasta" value="sequence.fasta" /> + <param name="input_gff3" value="sequence.gff3" /> + <output name="output" file="sequence.gff3.out" /> + </test> + </tests> + <help><![CDATA[ +**What it does** + +Finds rho-independent transcription terminators in bacterial genomes. +]]></help> + <citations> + <citation type="doi">doi:10.1186/gb-2007-8-2-r22</citation> + </citations> +</tool> |