Mercurial > repos > iuc > vapor
changeset 4:244812f5bd1f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
| author | iuc |
|---|---|
| date | Wed, 16 Nov 2022 13:41:01 +0000 |
| parents | f11d2dd29b2b |
| children | |
| files | test-data/HA_sample.fa test-data/output1_full.tab vapor.xml |
| diffstat | 3 files changed, 476 insertions(+), 38 deletions(-) [+] |
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--- a/test-data/HA_sample.fa Mon Oct 17 07:28:50 2022 +0000 +++ b/test-data/HA_sample.fa Wed Nov 16 13:41:01 2022 +0000 @@ -21,7 +21,7 @@ >cds:ADF80462 A/Gangwon/1805/2009 2009/11/18 HA H1N1 Human ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAATTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAGTTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGATAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCTTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGTTGAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA >cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human -ATGAAGGCAATACTAGTAGTTTTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA +atgaaggcaatactagtagttttgctatatacatttgcaaccgcaaatgcagacacattatgtataggttatcatgcgaacaattcaacagacactgtagacacagtactagaaaagaatgtaacagtaacacactctgttaaccttctagaagacaagcataacgggaaactatgcaaactaagaggggtagccccattgcatttgggtaaatgtaacattgctggctggatcctgggaaatccagagtgtgaatcactctccacagcaagctcatggtcctacattgtggaaacatctagttcagacaatggaacgtgttacccaggagatttcatcgattatgaggagctaagagagcaattgagctcagtgtcatcatttgaaaggtttgagatattccccaagacaagttcatggcccaatcatgactcgaacaaaggtgtaacggcagcatgtcctcatgctggagcaaaaagcttctacaaaaatttaatatggctagttaaaaaaggaaattcatacccaaagctcagcaaatcctacattaatgataaagggaaagaagtcctcgtgctatggggcattcaccatccatctactagtgctgaccaacaaagtctctatcagaatgcagatgcatatgtttttgtggggacatcaagatacagcaagaagttcaagccggaaatagcaataagacccaaagtgagggatcaagaagggagaatgaactattactggacactagtagagccgggagacaaaataacattcgaagcaactggaaatctagtggtaccgagatatgcattcgcaatggaaagaaatgctggatctggtattatcatttcagatacaccagtccacgattgcaatacaacttgtcagacacccaagggtgctataaacaccagcctcccatttcagaatatacatccgatcacaattggaaaatgtccaaaatatgtaaaaagcacaaaattgagactggccacaggattgaggaatgtcccgtctattcaatctagaggcctatttggggccattgccggtttcattgaaggggggtggacagggatggtagatggatggtacggttatcaccatcaaaatgagcaggggtcaggatatgcagccgacctgaagagcacacagaatgccattgacgagattactaacaaagtaaattctgttattgaaaagatgaatacacagttcacagcagtaggtaaagagttcaaccacctggaaaaaagaatagagaatttaaataaaaaagttgatgatggtttcctggacatttggacttacaatgccgaactgttggttctattggaaaatgaaagaactttggactaccacgattcaaatgtgaagaacttatatgaaaaggtaagaagccagttaaaaaacaatgccaaggaaattggaaacggctgctttgaattttaccacaaatgcgataacacgtgcatggaaagtgtcaaaaatgggacttatgactacccaaaatactcagaggaagcaaaattaaacagagaagaaatagatggggtaaagctggaatcaacaaggatttaccagattttggcgatctattcaactgtcgccagttcattggtactggtagtctccctgggggcaatcagtttctggatgtgctctaatgggtctctacagtgtagaatatgtatttaa >cds:AEO19882 A/Shanghai/2167T/2010 2010/01/15 HA H1N1 Human ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTACCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAATCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTAAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAGGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTACTGCTGACCAACAAAGTCTCTATCAGAATGCAGATACATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCAAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACGCAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAACCAGTTAAAAAACAATGCCAAGGAAATTGGAAATGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTTTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA >cds:AEX34318 A/Hue/H433/2008 2008/11/19 HA H1N1 Human @@ -997,4 +997,4 @@ >cds:ALK80386 A/India/DRDE_GWL897/2015 2015/03/15 HA H1N1 Human ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTACAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTGGAAGACAAGCATAACGGAAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGTTCATGGTCCTACATTGTGGAAACATCTAATTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCAATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCACGCTGGAGCAAAAAGCTTCTACAAAAACTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCCAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTGTGGGGCATTCACCATCCATCTACTACTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCACAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCGAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAGGTATGTAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTCGGGGCCATTGCCGGCTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAAAATGCCATTGACAAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTGGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTATCACGATTCAAATGTGAAGAACTTGTATGAAAAAGTAAGAAACCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAAAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGCTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA >cds:ALX27735 A/Cambodia/V1019341/2011 2011/10/11 HA H1N1 Human -ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTACCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAATCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATCTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAGGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTACTGCTGACCAACAAAGTCTCTATCAGAATGCAGATACATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAACAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTGGTGGTACCAAGATATGCATTCGCAATGGAAAGAGATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTTCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGCTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTACCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACAAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACTTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAGAAGGTAAGAAACCAGTTAAAAAACAATGCCAAGGAAATTGGAAATGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGTATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAAAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTTTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA \ No newline at end of file +ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTACCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAATCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATCTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAGGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTACTGCTGACCAACAAAGTCTCTATCAGAATGCAGATACATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAACAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTGGTGGTACCAAGATATGCATTCGCAATGGAAAGAGATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTTCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGCTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTACCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACAAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACTTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAGAAGGTAAGAAACCAGTTAAAAAACAATGCCAAGGAAATTGGAAATGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGTATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAAAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTTTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1_full.tab Wed Nov 16 13:41:01 2022 +0000 @@ -0,0 +1,415 @@ +0.9782480893592005 186719.0 1701 109.77013521457965 1000 >cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human +0.9770723104056437 186468.0 1701 109.62257495590829 1000 >cds:AGR50140 A/Mexico/24039/2009 2009/04/29 HA H1N1 Human +0.9706055261610818 186523.0 1701 109.6549088771311 1000 >cds:AFN19076 A/Singapore/ON361/2009 2009/06/21 HA H1N1 Human +0.9706055261610818 186471.0 1701 109.62433862433862 1000 >cds:ADO25192 A/Boston/658/2009 2009/11/13 HA H1N1 Human +0.9706055261610818 186468.0 1701 109.62257495590829 1000 >cds:ADZ04597 A/New York/3198/2009 2009/04/29 HA H1N1 Human +0.9706055261610818 186467.0 1701 109.62198706643152 1000 >cds:ACT79133 A/Japan/1070/2009 2009/06/29 HA H1N1 Human +0.9706055261610818 186466.0 1701 109.62139917695474 1000 >cds:ADO33202 A/Thailand/CU-H104/2009 2009/07/02 HA H1N1 Human +0.9706055261610818 186466.0 1701 109.62139917695474 1000 >cds:ADA83611 A/Argentina/HNRG21/2009 2009/07/01 HA H1N1 Human +0.9706055261610818 186464.0 1701 109.62022339800117 1000 >cds:AGI54938 A/Alaska/34/2009 2009/08/10 HA H1N1 Human +0.9706055261610818 186464.0 1701 109.62022339800117 1000 >cds:AEW10674 A/England/207/2009 2009/04/27 HA H1N1 Human +0.9706055261610818 186463.0 1701 109.6196355085244 1000 >cds:ADC32413 A/Ancona/17/2009 2009/07/17 HA H1N1 Human +0.9706055261610818 186463.0 1701 109.6196355085244 1000 >cds:AGI54501 A/Kansas/17/2009 2009/08/08 HA H1N1 Human +0.9706055261610818 186462.0 1701 109.61904761904762 1000 >cds:AFN18570 A/Singapore/ON1802/2009 2009/08/19 HA H1N1 Human +0.9706055261610818 186462.0 1701 109.61904761904762 1000 >cds:ADE20798 A/Managua/164.01/2009 2009/08/18 HA H1N1 Human +0.9706055261610818 186460.0 1701 109.61787184009407 1000 >cds:AFB70207 A/Argentina/7967/2009 2009/06/17 HA H1N1 Human +0.9706055261610818 186458.0 1701 109.6166960611405 1000 >cds:AEN68916 A/Cambodia/T354/2009 2009/09/11 HA H1N1 Human +0.9706055261610818 186458.0 1701 109.6166960611405 1000 >cds:ACT36656 A/New York/59/2009 2009/05/18 HA H1N1 Human +0.9706055261610818 186457.0 1701 109.61610817166373 1000 >cds:ADQ28037 A/Goias/69877/2009 2009/08/24 HA H1N1 Human +0.9706055261610818 186457.0 1701 109.61610817166373 1000 >cds:ACX31957 A/Myanmar/60/2009 2009// HA H1N1 Human +0.9706055261610818 186456.0 1701 109.61552028218695 1000 >cds:ADM95759 A/Finland/583/2009 2009/06/18 HA H1N1 Human +0.9706055261610818 186456.0 1701 109.61552028218695 1000 >cds:ACV33134 A/New York/3960/2009 2009/05/31 HA H1N1 Human +0.9706055261610818 186455.0 1701 109.61493239271017 1000 >cds:AGY41929 A/Singapore/464L/2009 2009/08/17 HA H1N1 Human +0.9706055261610818 186453.0 1701 109.6137566137566 1000 >cds:AFB70257 A/Argentina/8673/2009 2009/06/19 HA H1N1 Human +0.9706055261610818 186451.0 1701 109.61258083480305 1000 >cds:ACX35327 A/New York/4100/2009 2009/06/13 HA H1N1 Human +0.9700176366843033 186443.0 1701 109.60787771898883 1000 >cds:ADG59653 A/Moscow oblast/CRIE-IVD/2009 2009/09/10 HA H1N1 Human +0.9700176366843033 186426.0 1701 109.5978835978836 1000 >cds:AEO01079 A/England/610/2009 2009/07/02 HA H1N1 Human +0.9700176366843033 186419.0 1701 109.59376837154615 1000 >cds:ACV04378 A/New York/3747/2009 2009/05/16 HA H1N1 Human +0.9700176366843033 186416.0 1701 109.59200470311582 1000 >cds:AGI55265 A/Utah/34/2009 2009/07/11 HA H1N1 Human +0.9700176366843033 186415.0 1701 109.59141681363903 1000 >cds:AEO01143 A/England/92960005/2009 2009/07/15 HA H1N1 Human +0.9700176366843033 186397.0 1701 109.58083480305703 1000 >cds:ADI24519 A/Singapore/GP4247/2009 2009/11/06 HA H1N1 Human +0.9700176366843033 186386.0 1701 109.57436801881246 1000 >cds:ACZ17090 A/New York/4728/2009 2009/07/24 HA H1N1 Human +0.9700176366843033 186383.0 1701 109.57260435038212 1000 >cds:ADJ40494 A/Netherlands/2442b/2009 2009/11/05 HA H1N1 Human +0.9700176366843033 186352.0 1701 109.554379776602 1000 >cds:ADD97035 A/Wisconsin/629-D00036/2009 2009/09/15 HA H1N1 Human +0.9700176366843033 186349.0 1701 109.55261610817166 1000 >cds:AFN17910 A/Singapore/GP3009/2009 2009/08/14 HA H1N1 Human +0.9700176366843033 186347.0 1701 109.55144032921811 1000 >cds:AKM14702 A/Bangalore/2960-03/2009 2009/08/19 HA H1N1 Human +0.9700176366843033 186347.0 1701 109.55144032921811 1000 >cds:AFN18521 A/Singapore/ON1609/2009 2009/07/30 HA H1N1 Human +0.9700176366843033 186346.0 1701 109.55085243974133 1000 >cds:ADA83043 A/Novgorod/01/2009 2009// HA H1N1 Human +0.9700176366843033 186345.0 1701 109.55026455026454 1000 >cds:AEO01267 A/England/1006/2009 2009/09/22 HA H1N1 Human +0.9700176366843033 186343.0 1701 109.54908877131099 1000 >cds:ADM13071 A/Athens/INS390/2010 2010/01/14 HA H1N1 Human +0.9700176366843033 186342.0 1701 109.54850088183422 1000 >cds:ADB03613 A/Ankara/12/2009 2009/09/ HA H1N1 Human +0.9700176366843033 186339.0 1701 109.54673721340389 1000 >cds:ADJ80644 A/California/VRDL94/2009 2009/10/29 HA H1N1 Human +0.9700176366843033 186339.0 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A/California/99/2016 2016/03/25 HA H1N1 Human +0.9394473838918284 181296.0 1701 106.58201058201058 1000 >cds:AQW37206 A/Minnesota/09/2017 2017/01/30 HA H1N1 Human +0.9394473838918284 181181.0 1701 106.51440329218107 1000 >cds:ARO44116 A/Michigan/41/2017 2017/03/20 HA H1N1 Human +0.897119341563786 173890.0 1701 102.22810111699 1000 >cds:ACQ73203 A/Ohio/01/2007 2007/08/17 HA H1N1 Human
--- a/vapor.xml Mon Oct 17 07:28:50 2022 +0000 +++ b/vapor.xml Wed Nov 16 13:41:01 2022 +0000 @@ -1,6 +1,6 @@ -<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy2" profile="21.05"> +<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy3" profile="21.05"> <description> - Classify Influenza samples from raw short read sequence data + Classify Influenza samples from short reads sequence data </description> <macros> <token name="@TOOL_VERSION@">1.0.2</token> @@ -10,8 +10,22 @@ </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">vapor</requirement> + <!-- gawk only required for circumventing current bug in command line + tool => remove once fixed (see command section below) --> + <requirement type="package" version="5.1.0">gawk</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ + #set $total_refs = int($fasta_file.metadata.sequences) + + ## The next two lines for on the fly uppercasing are a workaround for a bug + ## in vapor 1.0.2, which caused sequence comparisons to be case-sensitive. + ## Got fixed upstream in: + ## https://github.com/connor-lab/vapor/commit/b5ec5857cbf53ed45ca7487dac2b4b85ecfe33ea + ## but unfortunately no release has been tagged since. + ## Remove with next release!! + awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' '$fasta_file' > ref_upper.fa && + #set $fasta_file = 'ref_upper.fa' + #if str($fastq_input.fastq_input_selector) == "paired" #set r1_ext = $fastq_input.fastq1.extension #set r2_ext = $fastq_input.fastq2.extension @@ -27,54 +41,56 @@ ln -s '$fastq_input.fastq_single' fastq1.$r1_ext && #end if vapor.py - --return_best_n $opt.return_best_n + #if int($return_best_n) > 0 + --return_best_n $return_best_n + #else + --return_best_n $total_refs + #end if #if $output_type == "fasta" --return_seqs #end if - -k '$opt.kmer_length' - -t '$opt.score_threshold' - -c '$opt.min_kmer_cov' - -m '$opt.min_kmer_prop' + -k $opt.kmer_length + -t $opt.threshold + -c $opt.min_kmer_cov + -m $opt.min_kmer_prop -fa '$fasta_file' - -fq - fastq1.$r1_ext + -fq fastq1.$r1_ext #if str($fastq_input.fastq_input_selector) in ["paired", "paired_collection"] fastq2.$r2_ext #end if - -f '$opt.top_seed_frac' - -q + -f $opt.top_seed_frac > out_file - ]]> </command> + ]]></command> <inputs> - <param name="fasta_file" format="fasta" type="data" label="FASTA file" help="Raw short read sequences (full length reference segment sequences)" /> + <param name="fasta_file" format="fasta" type="data" label="Reference sequences" help="Select a multisample fasta dataset with reference sequences to base classification on." /> <conditional name="fastq_input"> - <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> - <option value="single">Single</option> - <option value="paired">Paired</option> - <option value="paired_collection">Paired Collection</option> + <param name="fastq_input_selector" type="select" label="Type of sequencing data"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + <option value="paired_collection">Paired-end as collection</option> </param> <when value="single"> - <param name="fastq_single" format="fastqsanger,fastqsanger.gz" type="data" label="FASTQ file" help="Raw short read sequences (full length reference segment sequences)" /> + <param name="fastq_single" format="fastqsanger,fastqsanger.gz" type="data" label="Sequenced reads" help="Specify the sequenced reads dataset." /> </when> <when value="paired"> - <param name="fastq1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify reads dataset with forward reads"/> - <param name="fastq2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify reads dataset with reverse reads"/> + <param name="fastq1" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads" help="Specify the sequenced reads dataset with forward reads."/> + <param name="fastq2" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads" help="Specify the sequenced reads dataset with reverse reads."/> </when> <when value="paired_collection"> - <param name="fastq_pairs" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="Dataset collection with forward and reverse reads"/> + <param name="fastq_pairs" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Paired collection of sequenced reads" help="Select a collection with forward and reverse reads."/> </when> </conditional> - <param name="output_type" type="select" label="Output type"> - <option value="scores" selected="true">Return scores only</option> - <option value="fasta">Return FASTA only</option> + <param name="output_type" type="select" label="Desired output"> + <option value="scores" selected="true">Return scores of best matches</option> + <option value="fasta">Return FASTA sequences of best matches</option> </param> + <param name="return_best_n" type="integer" min="0" value="1" label="Limit number of reported matches to" help="Determines the maximum number of candidate matches sorted by score that will be reported. Set to zero to get all candidate matches reported." /> <section name="opt" title="Optional arguments" expanded="true"> - <param name="return_best_n" type="integer" min="1" value="1" label="Returns the highest scoring n queries" help="A list of the best n queries instead of only the highest scoring query" /> - <param name="kmer_length" type="integer" min="5" max="30" value="21" label="Kmer Length" help="" /> - <param name="score_threshold" type="float" min="0.0" max="1.0" value="0.2" label="Read kmer filtering threshold" help="" /> - <param name="min_kmer_cov" type="integer" value="5" label="Min coverage kmer culling" help="Minimum coverage kmer culling" /> - <param name="min_kmer_prop" type="float" value="0.1" label="Min kmer proportion" help="Minimum proportion of matched kmers allowed for queries" /> - <param name="top_seed_frac" type="float" min="0.0" max="1.0" value="0.2" label="Fraction of best seeds to extend" help="" /> + <param argument="-k" name="kmer_length" type="integer" min="5" max="30" value="21" label="Kmer Length" help="Generate k-mers of this length from the reference sequences and the sequenced reads. Note: smaller k-mer sizes come at the cost of decreased specificity and k-mer sizes below 21 have an increased risk of contaminating sequences getting analyzed. Only decrease the default (21) if you know your sample is pure (i.e., sequenced reads represent viral reads only), or if you have increased --threshold sufficiently." /> + <param argument="--threshold" type="float" min="0" max="1" value="0.2" label="Read kmer filtering threshold" help="Sequenced reads that don't have at least this proportion of their k-mers matching k-mers generated from the reference sequences will not be considered in the analysis; default: 0.2" /> + <param argument="--min_kmer_cov" type="integer" min="1" value="5" label="Coverage threshold for k-mer culling" help="Minimum coverage by sequenced reads for a reference k-mer to be kept during culling; default: 5" /> + <param argument="--min_kmer_prop" type="float" min="0" max="1" value="0.1" label="Minimum k-mer proportion" help="Minimum proportion of matching kmers required for queries; default: 0.1" /> + <param argument="--top_seed_frac" type="float" min="0" max="1" value="1" label="Fraction of best seeds to extend" help="Of the queries still considered after applying the --min_kmer_prop filter above, the tool will calculate and report scores only for this fraction. Lowering this value leads to shorter runtime because fewer scores will have to be calculated, but also to fewer results getting reported. CAVEAT: this version of the tool will round down the result of applying this parameter so it is possible to end up with zero queries to be considered further. Change only if runtime is an issue!" /> </section> </inputs> <outputs> @@ -99,6 +115,15 @@ </test> <test expect_num_outputs="1"> <conditional name="fastq_input"> + <param name="fastq_input_selector" value="single" /> + <param name="fastq_single" ftype="fastq" value="test_reads.fq" /> + </conditional> + <param name="fasta_file" value="HA_sample.fa" /> + <param name="return_best_n" value="0" /> + <output name="output_scores" file="output1_full.tab" /> + </test> + <test expect_num_outputs="1"> + <conditional name="fastq_input"> <param name="fastq_input_selector" value="paired" /> <param name="fastq1" ftype="fastq" value="test_reads.fq" /> <param name="fastq2" ftype="fastq" value="test_reads2.fq" /> @@ -122,7 +147,7 @@ <param name="fasta_file" value="HA_sample.fa" /> <section name="opt"> <param name="kmer_length" value="29" /> - <param name="score_threshold" value="0.5" /> + <param name="threshold" value="0.5" /> <param name="min_kmer_cov" value="7" /> <param name="min_kmer_prop" value="0.5" /> <param name="top_seed_frac" value="0.5" /> @@ -136,9 +161,7 @@ </conditional> <param name="fasta_file" value="HA_sample.fa" /> <param name="output_type" value="fasta" /> - <section name="opt"> - <param name="return_best_n" value="3" /> - </section> + <param name="return_best_n" value="3" /> <output name="output_fasta" file="output5.fa" /> </test> </tests> @@ -146,11 +169,11 @@ **What it does** VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. -VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. +VAPOR works on a fasta file of full-length reference sequences for a given genome segment and a set of sequenced reads, and attempts to retrieve the reference that is closest to the sequenced strain. `sub_sample` is not an option here (compared to the tool on GitHub), since you can always build a workflow that preprocesses your reads to a (random) subsample. You can use this output as your reads file for VAPOR. ]]> </help> <citations> <citation type="doi">10.1093/bioinformatics/btz814</citation> </citations> -</tool> \ No newline at end of file +</tool>