# HG changeset patch # User iuc # Date 1668606061 0 # Node ID 244812f5bd1ff96ffb3bd0025419f571a2f27060 # Parent f11d2dd29b2bbd7e1d30e18f08bbd8c94fd8f15a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583 diff -r f11d2dd29b2b -r 244812f5bd1f test-data/HA_sample.fa --- 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 diff -r f11d2dd29b2b -r 244812f5bd1f test-data/output1_full.tab --- /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 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2016/04/25 HA H1N1 Human +0.9394473838918284 181366.0 1701 106.62316284538507 1000 >cds:ANM94264 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 diff -r f11d2dd29b2b -r 244812f5bd1f vapor.xml --- 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 @@ - + - Classify Influenza samples from raw short read sequence data + Classify Influenza samples from short reads sequence data 1.0.2 @@ -10,8 +10,22 @@ vapor + + gawk /) {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 - ]]> + ]]> - + - - - - + + + + - + - - + + - + - - - + + + +
- - - - - - + + + + +
@@ -99,6 +115,15 @@ + + + + + + + + + @@ -122,7 +147,7 @@
- + @@ -136,9 +161,7 @@ -
- -
+ @@ -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. ]]> 10.1093/bioinformatics/btz814 - \ No newline at end of file +