Repository 'vapor'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/vapor

Changeset 4:244812f5bd1f (2022-11-16)
Previous changeset 3:f11d2dd29b2b (2022-10-17)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
modified:
test-data/HA_sample.fa
vapor.xml
added:
test-data/output1_full.tab
b
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
b
b'@@ -21,7 +21,7 @@\n >cds:ADF80462 A/Gangwon/1805/2009 2009/11/18 HA H1N1 Human\n ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAATTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAGTTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGATAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCTTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGTTGAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA\n >cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n-ATGAAGGCAATACTAGTAGTTTTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA\n+atgaaggcaatactagtagttttgctatatacatttgcaaccgcaaatgcagacacattatgtataggttatcatgcgaacaattcaacagacactgtagacacagtactagaaaagaatgtaacagtaacacactctgttaaccttctagaagacaagcataacgggaaactatgcaaactaagaggggtagccccattgcatttgggtaaatgtaacattgctggctggatcctgggaaatccagagtgtgaatcactctccacagcaagctcatggtcctacattgtggaaacatctagttcagacaatggaacgtgttacccaggagatttcatcgattatgaggagctaagagagcaattgagctcagtgtcatcatttgaaaggtttgagatattccccaagacaagttcatggcccaatcatgactcgaacaaaggtgtaacggcagca'..b'AAAGATGAATACACAGTTCACAGCAGTGGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTATCACGATTCAAATGTGAAGAACTTGTATGAAAAAGTAAGAAACCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAAAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGCTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA\n >cds:ALX27735 A/Cambodia/V1019341/2011 2011/10/11 HA H1N1 Human\n-ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTACCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAATCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATCTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAGGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTACTGCTGACCAACAAAGTCTCTATCAGAATGCAGATACATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAACAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTGGTGGTACCAAGATATGCATTCGCAATGGAAAGAGATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTTCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGCTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTACCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACAAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACTTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAGAAGGTAAGAAACCAGTTAAAAAACAATGCCAAGGAAATTGGAAATGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGTATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAAAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTTTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA\n\\ No newline at end of file\n+ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTACCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAATCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATCTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAGGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTACTGCTGACCAACAAAGTCTCTATCAGAATGCAGATACATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAACAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTGGTGGTACCAAGATATGCATTCGCAATGGAAAGAGATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTTCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGCTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTACCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACAAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACTTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAGAAGGTAAGAAACCAGTTAAAAAACAATGCCAAGGAAATTGGAAATGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGTATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAAAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTTTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA\n'
b
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
b
b'@@ -0,0 +1,415 @@\n+0.9782480893592005\t186719.0\t1701\t109.77013521457965\t1000\t>cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human\n+0.9770723104056437\t186468.0\t1701\t109.62257495590829\t1000\t>cds:AGR50140 A/Mexico/24039/2009 2009/04/29 HA H1N1 Human\n+0.9706055261610818\t186523.0\t1701\t109.6549088771311\t1000\t>cds:AFN19076 A/Singapore/ON361/2009 2009/06/21 HA H1N1 Human\n+0.9706055261610818\t186471.0\t1701\t109.62433862433862\t1000\t>cds:ADO25192 A/Boston/658/2009 2009/11/13 HA H1N1 Human\n+0.9706055261610818\t186468.0\t1701\t109.62257495590829\t1000\t>cds:ADZ04597 A/New York/3198/2009 2009/04/29 HA H1N1 Human\n+0.9706055261610818\t186467.0\t1701\t109.62198706643152\t1000\t>cds:ACT79133 A/Japan/1070/2009 2009/06/29 HA H1N1 Human\n+0.9706055261610818\t186466.0\t1701\t109.62139917695474\t1000\t>cds:ADO33202 A/Thailand/CU-H104/2009 2009/07/02 HA H1N1 Human\n+0.9706055261610818\t186466.0\t1701\t109.62139917695474\t1000\t>cds:ADA83611 A/Argentina/HNRG21/2009 2009/07/01 HA H1N1 Human\n+0.9706055261610818\t186464.0\t1701\t109.62022339800117\t1000\t>cds:AGI54938 A/Alaska/34/2009 2009/08/10 HA H1N1 Human\n+0.9706055261610818\t186464.0\t1701\t109.62022339800117\t1000\t>cds:AEW10674 A/England/207/2009 2009/04/27 HA H1N1 Human\n+0.9706055261610818\t186463.0\t1701\t109.6196355085244\t1000\t>cds:ADC32413 A/Ancona/17/2009 2009/07/17 HA H1N1 Human\n+0.9706055261610818\t186463.0\t1701\t109.6196355085244\t1000\t>cds:AGI54501 A/Kansas/17/2009 2009/08/08 HA H1N1 Human\n+0.9706055261610818\t186462.0\t1701\t109.61904761904762\t1000\t>cds:AFN18570 A/Singapore/ON1802/2009 2009/08/19 HA H1N1 Human\n+0.9706055261610818\t186462.0\t1701\t109.61904761904762\t1000\t>cds:ADE20798 A/Managua/164.01/2009 2009/08/18 HA H1N1 Human\n+0.9706055261610818\t186460.0\t1701\t109.61787184009407\t1000\t>cds:AFB70207 A/Argentina/7967/2009 2009/06/17 HA H1N1 Human\n+0.9706055261610818\t186458.0\t1701\t109.6166960611405\t1000\t>cds:AEN68916 A/Cambodia/T354/2009 2009/09/11 HA H1N1 Human\n+0.9706055261610818\t186458.0\t1701\t109.6166960611405\t1000\t>cds:ACT36656 A/New York/59/2009 2009/05/18 HA H1N1 Human\n+0.9706055261610818\t186457.0\t1701\t109.61610817166373\t1000\t>cds:ADQ28037 A/Goias/69877/2009 2009/08/24 HA H1N1 Human\n+0.9706055261610818\t186457.0\t1701\t109.61610817166373\t1000\t>cds:ACX31957 A/Myanmar/60/2009 2009// HA H1N1 Human\n+0.9706055261610818\t186456.0\t1701\t109.61552028218695\t1000\t>cds:ADM95759 A/Finland/583/2009 2009/06/18 HA H1N1 Human\n+0.9706055261610818\t186456.0\t1701\t109.61552028218695\t1000\t>cds:ACV33134 A/New York/3960/2009 2009/05/31 HA H1N1 Human\n+0.9706055261610818\t186455.0\t1701\t109.61493239271017\t1000\t>cds:AGY41929 A/Singapore/464L/2009 2009/08/17 HA H1N1 Human\n+0.9706055261610818\t186453.0\t1701\t109.6137566137566\t1000\t>cds:AFB70257 A/Argentina/8673/2009 2009/06/19 HA H1N1 Human\n+0.9706055261610818\t186451.0\t1701\t109.61258083480305\t1000\t>cds:ACX35327 A/New York/4100/2009 2009/06/13 HA H1N1 Human\n+0.9700176366843033\t186443.0\t1701\t109.60787771898883\t1000\t>cds:ADG59653 A/Moscow oblast/CRIE-IVD/2009 2009/09/10 HA H1N1 Human\n+0.9700176366843033\t186426.0\t1701\t109.5978835978836\t1000\t>cds:AEO01079 A/England/610/2009 2009/07/02 HA H1N1 Human\n+0.9700176366843033\t186419.0\t1701\t109.59376837154615\t1000\t>cds:ACV04378 A/New York/3747/2009 2009/05/16 HA H1N1 Human\n+0.9700176366843033\t186416.0\t1701\t109.59200470311582\t1000\t>cds:AGI55265 A/Utah/34/2009 2009/07/11 HA H1N1 Human\n+0.9700176366843033\t186415.0\t1701\t109.59141681363903\t1000\t>cds:AEO01143 A/England/92960005/2009 2009/07/15 HA H1N1 Human\n+0.9700176366843033\t186397.0\t1701\t109.58083480305703\t1000\t>cds:ADI24519 A/Singapore/GP4247/2009 2009/11/06 HA H1N1 Human\n+0.9700176366843033\t186386.0\t1701\t109.57436801881246\t1000\t>cds:ACZ17090 A/New York/4728/2009 2009/07/24 HA H1N1 Human\n+0.9700176366843033\t186383.0\t1701\t109.57260435038212\t1000\t>cds:ADJ40494 A/Netherlands/2442b/2009 2009/11/05 HA H1N1 Human\n+0.9700176366843033\t186352.0\t1701\t109.554379776602\t1000\t>cds:ADD97035 A/Wisconsin/629-D00036/2009 2009/09/15 HA H1N1 Human\n+0.9700176366843033\t186349.0\t1701\t109.55261610817166\t1000\t>cds:AFN17910 A/Singapore/GP3009/2009 2009'..b'uman\n+0.9447383891828336\t182368.0\t1701\t107.21222810111699\t1000\t>cds:APR73940 A/South Korea/5553/2016 2016/02/22 HA H1N1 Human\n+0.9447383891828336\t182360.0\t1701\t107.20752498530277\t1000\t>cds:AOT88328 A/Connecticut/23/2016 2016/03/23 HA H1N1 Human\n+0.9441504997060552\t182357.0\t1701\t107.20576131687243\t1000\t>cds:ANM87731 A/Nevada/10/2016 2016/01/26 HA H1N1 Human\n+0.9441504997060552\t182348.0\t1701\t107.20047031158143\t1000\t>cds:ANM87369 A/Alaska/03/2016 2016/01/18 HA H1N1 Human\n+0.9441504997060552\t182311.0\t1701\t107.17871840094062\t1000\t>cds:APR73830 A/Florida/5443/2016 2016/03/09 HA H1N1 Human\n+0.9441504997060552\t182271.0\t1701\t107.1552028218695\t1000\t>cds:ANE26819 A/Maryland/21/2015 2015/12/12 HA H1N1 Human\n+0.9441504997060552\t182253.0\t1701\t107.14462081128748\t1000\t>cds:AOT87283 A/Indiana/39/2016 2016/04/10 HA H1N1 Human\n+0.9441504997060552\t182248.0\t1701\t107.14168136390359\t1000\t>cds:APR73861 A/North Carolina/5474/2016 2016/03/11 HA H1N1 Human\n+0.9441504997060552\t182233.0\t1701\t107.13286302175192\t1000\t>cds:ANM88720 A/Washington/28/2016 2016/02/19 HA H1N1 Human\n+0.9435626102292769\t182189.0\t1701\t107.10699588477367\t1000\t>cds:AQS98409 A/Idaho/08/2017 2017/01/21 HA H1N1 Human\n+0.9435626102292769\t182112.0\t1701\t107.06172839506173\t1000\t>cds:AOT92678 A/Connecticut/17/2016 2016/04/06 HA H1N1 Human\n+0.9435626102292769\t182112.0\t1701\t107.06172839506173\t1000\t>cds:AOT87580 A/Maine/20/2016 2016/04/29 HA H1N1 Human\n+0.9435626102292769\t182103.0\t1701\t107.05643738977072\t1000\t>cds:APQ44646 A/Alabama/5358/2016 2016/03/22 HA H1N1 Human\n+0.9435626102292769\t182080.0\t1701\t107.04291593180483\t1000\t>cds:APF46418 A/Japan/5013/2016 2016/02/10 HA H1N1 Human\n+0.9429747207524986\t182163.0\t1701\t107.09171075837743\t1000\t>cds:ANW83139 A/California/NHRC_W7416A/2016 2016/04/22 HA H1N1 Human\n+0.9429747207524986\t182161.0\t1701\t107.09053497942386\t1000\t>cds:AOT88493 A/North Carolina/49/2016 2016/05/12 HA H1N1 Human\n+0.9429747207524986\t182156.0\t1701\t107.08759553203997\t1000\t>cds:APG55968 A/New Jersey/5134/2016 2016/03/04 HA H1N1 Human\n+0.9429747207524986\t182065.0\t1701\t107.03409758965314\t1000\t>cds:AOT93206 A/California/117/2016 2016/05/19 HA H1N1 Human\n+0.9429747207524986\t181992.0\t1701\t106.99118165784833\t1000\t>cds:ANM93967 A/Illinois/14/2016 2016/02/24 HA H1N1 Human\n+0.9429747207524986\t181991.0\t1701\t106.99059376837154\t1000\t>cds:AOT92623 A/Pennsylvania/54/2016 2016/03/06 HA H1N1 Human\n+0.9423868312757202\t182084.0\t1701\t107.04526748971193\t1000\t>cds:APG56023 A/Arizona/5189/2016 2016/03/08 HA H1N1 Human\n+0.9423868312757202\t182074.0\t1701\t107.03938859494416\t1000\t>cds:ANM92735 A/Pennsylvania/36/2016 2016/03/17 HA H1N1 Human\n+0.9423868312757202\t181948.0\t1701\t106.96531452087008\t1000\t>cds:AOZ81520 A/Florida/72/2016 2016/08/28 HA H1N1 Human\n+0.9423868312757202\t181942.0\t1701\t106.96178718400941\t1000\t>cds:ANE28493 A/Arkansas/01/2016 2016/01/09 HA H1N1 Human\n+0.9435626102292769\t181585.0\t1701\t106.75191064079954\t1000\t>cds:ANE26954 A/Hawaii/59/2015 2015/09/18 HA H1N1 Human\n+0.9417989417989417\t181722.0\t1701\t106.83245149911816\t1000\t>cds:AQW35837 A/Iowa/04/2017 2017/01/18 HA H1N1 Human\n+0.93885949441505\t181895.0\t1701\t106.93415637860082\t1000\t>cds:ANE27294 A/California/120/2015 2015/12/28 HA H1N1 Human\n+0.940623162845385\t181459.0\t1701\t106.67783656672546\t1000\t>cds:AQW36171 A/Indiana/10/2017 2017/01/27 HA H1N1 Human\n+0.9376837154614932\t181876.0\t1701\t106.92298647854203\t1000\t>cds:ARI69622 A/Porto Alegre/LACENRS-599/2016 2016/04/08 HA H1N1 Human\n+0.9376837154614932\t181845.0\t1701\t106.9047619047619\t1000\t>cds:ARI68577 A/Canoas/LACENRS-1105/2016 2016/04/25 HA H1N1 Human\n+0.9394473838918284\t181366.0\t1701\t106.62316284538507\t1000\t>cds:ANM94264 A/California/99/2016 2016/03/25 HA H1N1 Human\n+0.9394473838918284\t181296.0\t1701\t106.58201058201058\t1000\t>cds:AQW37206 A/Minnesota/09/2017 2017/01/30 HA H1N1 Human\n+0.9394473838918284\t181181.0\t1701\t106.51440329218107\t1000\t>cds:ARO44116 A/Michigan/41/2017 2017/03/20 HA H1N1 Human\n+0.897119341563786\t173890.0\t1701\t102.22810111699\t1000\t>cds:ACQ73203 A/Ohio/01/2007 2007/08/17 HA H1N1 Human\n'
b
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
[
b'@@ -1,6 +1,6 @@\n-<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy2" profile="21.05">\n+<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy3" profile="21.05">\n     <description>\n-        Classify Influenza samples from raw short read sequence data\n+        Classify Influenza samples from short reads sequence data\n     </description>\n     <macros>\n         <token name="@TOOL_VERSION@">1.0.2</token>\n@@ -10,8 +10,22 @@\n     </xrefs>\n     <requirements>\n         <requirement type="package" version="@TOOL_VERSION@">vapor</requirement>\n+        <!-- gawk only required for circumventing current bug in command line\n+        tool => remove once fixed (see command section below) -->\n+        <requirement type="package" version="5.1.0">gawk</requirement>\n     </requirements>\n     <command detect_errors="exit_code"><![CDATA[\n+        #set $total_refs = int($fasta_file.metadata.sequences)\n+\n+        ## The next two lines for on the fly uppercasing are a workaround for a bug\n+        ## in vapor 1.0.2, which caused sequence comparisons to be case-sensitive.\n+        ## Got fixed upstream in:\n+        ## https://github.com/connor-lab/vapor/commit/b5ec5857cbf53ed45ca7487dac2b4b85ecfe33ea\n+        ## but unfortunately no release has been tagged since.\n+        ## Remove with next release!!\n+        awk \'{ if ($0 !~ />/) {print toupper($0)} else {print $0} }\' \'$fasta_file\' > ref_upper.fa &&\n+        #set $fasta_file = \'ref_upper.fa\'\n+\n         #if str($fastq_input.fastq_input_selector) == "paired"\n             #set r1_ext = $fastq_input.fastq1.extension\n             #set r2_ext = $fastq_input.fastq2.extension\n@@ -27,54 +41,56 @@\n             ln -s \'$fastq_input.fastq_single\' fastq1.$r1_ext &&\n         #end if\n         vapor.py\n-            --return_best_n $opt.return_best_n\n+            #if int($return_best_n) > 0\n+                --return_best_n $return_best_n\n+            #else\n+                --return_best_n $total_refs\n+            #end if\n             #if $output_type == "fasta"\n                 --return_seqs\n             #end if\n-            -k \'$opt.kmer_length\'\n-            -t \'$opt.score_threshold\'\n-            -c \'$opt.min_kmer_cov\'\n-            -m \'$opt.min_kmer_prop\'\n+            -k $opt.kmer_length\n+            -t $opt.threshold\n+            -c $opt.min_kmer_cov\n+            -m $opt.min_kmer_prop\n             -fa \'$fasta_file\'\n-            -fq \n-            fastq1.$r1_ext\n+            -fq fastq1.$r1_ext\n             #if str($fastq_input.fastq_input_selector) in ["paired", "paired_collection"]\n                 fastq2.$r2_ext\n             #end if\n-            -f \'$opt.top_seed_frac\'\n-            -q\n+            -f $opt.top_seed_frac\n         > out_file\n-    ]]>    </command>\n+    ]]></command>\n     <inputs>\n-        <param name="fasta_file" format="fasta" type="data" label="FASTA file" help="Raw short read sequences (full length reference segment sequences)" />\n+        <param name="fasta_file" format="fasta" type="data" label="Reference sequences" help="Select a multisample fasta dataset with reference sequences to base classification on." />\n         <conditional name="fastq_input">\n-            <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">\n-                <option value="single">Single</option>\n-                <option value="paired">Paired</option>\n-                <option value="paired_collection">Paired Collection</option>\n+            <param name="fastq_input_selector" type="select" label="Type of sequencing data">\n+                <option value="single">Single-end</option>\n+                <option value="paired">Paired-end</option>\n+                <option value="paired_collection">Paired-end as collection</option>\n             </param>\n             <when value="single">\n-                <param name="fastq_single" format="fastqsanger,fastqsanger.gz" type="data" label="FASTQ file" help="Raw short read sequences (full le'..b'ue="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" />\n+            <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" />\n+            <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" />\n+            <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!" />\n         </section>\n     </inputs>\n     <outputs>\n@@ -99,6 +115,15 @@\n         </test>\n         <test expect_num_outputs="1">\n             <conditional name="fastq_input">\n+                <param name="fastq_input_selector" value="single" />\n+                <param name="fastq_single" ftype="fastq" value="test_reads.fq" />\n+            </conditional>\n+            <param name="fasta_file" value="HA_sample.fa" />\n+            <param name="return_best_n" value="0" />\n+            <output name="output_scores" file="output1_full.tab" />\n+        </test>\n+        <test expect_num_outputs="1">\n+            <conditional name="fastq_input">\n                 <param name="fastq_input_selector" value="paired" />\n                 <param name="fastq1" ftype="fastq" value="test_reads.fq" />\n                 <param name="fastq2" ftype="fastq" value="test_reads2.fq" />\n@@ -122,7 +147,7 @@\n             <param name="fasta_file" value="HA_sample.fa" />\n             <section name="opt">\n                 <param name="kmer_length" value="29" />\n-                <param name="score_threshold" value="0.5" />\n+                <param name="threshold" value="0.5" />\n                 <param name="min_kmer_cov" value="7" />\n                 <param name="min_kmer_prop" value="0.5" />\n                 <param name="top_seed_frac" value="0.5" />\n@@ -136,9 +161,7 @@\n             </conditional>\n             <param name="fasta_file" value="HA_sample.fa" />\n             <param name="output_type" value="fasta" />\n-            <section name="opt">\n-                <param name="return_best_n" value="3" />\n-            </section>\n+            <param name="return_best_n" value="3" />\n             <output name="output_fasta" file="output5.fa" />\n         </test>\n     </tests>\n@@ -146,11 +169,11 @@\n **What it does**\n \n VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis.\n-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.\n+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.\n \n `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.\n     ]]>    </help>\n     <citations>\n         <citation type="doi">10.1093/bioinformatics/btz814</citation>\n     </citations>\n-</tool>\n\\ No newline at end of file\n+</tool>\n'