# HG changeset patch
# User iuc
# Date 1649340242 0
# Node ID e10b5eebd4153e0c67df2b44af1a313568278420
# Parent 3c3c359d9b852cc16f5ed7c003cdd1a2f59e8a8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
diff -r 3c3c359d9b85 -r e10b5eebd415 export_fasta.xml
--- a/export_fasta.xml Mon Apr 04 10:22:24 2022 +0000
+++ b/export_fasta.xml Thu Apr 07 14:04:02 2022 +0000
@@ -16,7 +16,7 @@
-
+
diff -r 3c3c359d9b85 -r e10b5eebd415 macros.xml
--- a/macros.xml Mon Apr 04 10:22:24 2022 +0000
+++ b/macros.xml Thu Apr 07 14:04:02 2022 +0000
@@ -1,5 +1,5 @@
- 2.7.17
+ 2.7.22
0
22.01
@@ -22,8 +22,8 @@
-
-
+
+
diff -r 3c3c359d9b85 -r e10b5eebd415 test-data/AalborgWWTPs.2010.rds
Binary file test-data/AalborgWWTPs.2010.rds has changed
diff -r 3c3c359d9b85 -r e10b5eebd415 test-data/AalborgWWTPs.2011.rds
Binary file test-data/AalborgWWTPs.2011.rds has changed
diff -r 3c3c359d9b85 -r e10b5eebd415 test-data/AalborgWWTPs.tax.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/AalborgWWTPs.tax.tsv Thu Apr 07 14:04:02 2022 +0000
@@ -0,0 +1,201 @@
+Kingdom Phylum Class Order Family Genus Species OTU
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Lachnospiraceae g__Acetitomaculum s__ OTU_8735
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__Ruminococcaceae UCG-005 s__ OTU_13382
+k__Bacteria p__Bacteroidetes c__Cytophagia o__Cytophagales f__Cytophagaceae g__Dyadobacter s__ OTU_5516
+k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Nitrosomonadales f__Nitrosomonadaceae g__Nitrosomonas s__ OTU_8315
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Micrococcales f__Intrasporangiaceae g__Tetrasphaera s__ OTU_10522
+k__Bacteria p__Proteobacteria c__Gammaproteobacteria o__Xanthomonadales f__Xanthomonadaceae OTU_11040
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Desulfobacterales f__Desulfobacteraceae g__Desulforegula s__ OTU_7263
+k__Bacteria p__Firmicutes c__Bacilli o__Bacillales f__Planococcaceae g__Rummeliibacillus s__ OTU_13379
+k__Bacteria p__Hydrogenedentes c__ o__ f__ g__ s__ OTU_1418
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Lachnospiraceae g__Fusicatenibacter s__ OTU_556
+k__Bacteria p__Parcubacteria c__ o__ f__ g__ s__ OTU_6869
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__Ruminiclostridium 1 s__ OTU_10171
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Micrococcales f__Dermatophilaceae g__uncultured s__ OTU_2830
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__AKYH767 g__ s__ OTU_4232
+k__Bacteria p__Planctomycetes c__Planctomycetacia o__Planctomycetales f__Planctomycetaceae OTU_12831
+k__Bacteria p__Acidobacteria c__Holophagae o__Holophagales f__Holophagaceae OTU_613
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Propionibacteriaceae g__Brooklawnia s__ OTU_3625
+k__Bacteria p__Chloroflexi c__Chloroflexia o__Chloroflexales f__Roseiflexaceae g__ s__ OTU_3605
+k__Bacteria p__Actinobacteria c__Actinobacteria o__PeM15 f__PeM15 g__ s__ OTU_11148
+k__Bacteria p__Chloroflexi c__Caldilineae o__Caldilineales f__Caldilineaceae g__uncultured s__ OTU_656
+k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Rhodocyclales f__Rhodocyclaceae g__Sulfuritalea s__ OTU_4382
+k__Bacteria OTU_3834
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales OTU_13127
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales OTU_4528
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Myxococcales f__Blfdi19 g__ s__ OTU_4485
+k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Lactobacillaceae g__Lactobacillus s__ OTU_12265
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae OTU_11820
+k__Bacteria p__Chloroflexi c__Anaerolineae o__Anaerolineales f__Anaerolineaceae g__uncultured s__ OTU_4093
+k__Bacteria p__Bacteroidetes c__Flavobacteriia o__Flavobacteriales f__Flavobacteriaceae g__Flavobacterium s__ OTU_8360
+k__Bacteria p__Firmicutes c__Negativicutes o__Selenomonadales f__Veillonellaceae OTU_15123
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Desulfobacterales f__Desulfobacteraceae OTU_11928
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhodospirillales f__Acetobacteraceae g__Acidicaldus s__ OTU_11334
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Myxococcales f__mle1-27 g__ s__ OTU_4511
+k__Bacteria p__Chloroflexi c__Anaerolineae o__Anaerolineales f__Anaerolineaceae g__uncultured s__ OTU_3265
+k__Bacteria p__Actinobacteria OTU_2991
+k__Bacteria p__Chloroflexi c__Caldilineae o__Caldilineales f__Caldilineaceae g__Candidatus Defluviifilum s__ OTU_522
+k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Nitrosomonadales f__Nitrosomonadaceae g__Nitrosomonas s__ OTU_11832
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__Ruminococcaceae UCG-010 s__ OTU_6358
+k__Bacteria p__Saccharibacteria c__Unknown Class o__Unknown Order f__SBR2060 g__SBR2113 s__ OTU_3611
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales OTU_1408
+k__Bacteria p__Bacteroidetes OTU_7471
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__Subdoligranulum s__ OTU_14124
+k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Lactobacillaceae g__Lactobacillus s__ OTU_13012
+k__Bacteria p__Candidate division SR1 c__ o__ f__ g__ s__ OTU_8113
+k__Bacteria p__Cyanobacteria c__Cyanobacteria o__SubsectionIII f__FamilyI OTU_11414
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Micrococcales f__Microbacteriaceae OTU_2232
+k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Lactobacillaceae g__Lactobacillus s__ OTU_13504
+k__Bacteria p__Chloroflexi c__Caldilineae o__Caldilineales f__Caldilineaceae g__uncultured s__ OTU_173
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Lachnospiraceae OTU_11006
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Saprospiraceae g__uncultured s__ OTU_9035
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales OTU_8165
+k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Burkholderiales f__Comamonadaceae g__Ramlibacter s__ OTU_1707
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rickettsiales f__TK34 g__ s__ OTU_4805
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhizobiales f__Bradyrhizobiaceae g__Bosea s__ OTU_7801
+k__Bacteria p__Hydrogenedentes c__ o__ f__ g__ s__ OTU_6106
+k__Bacteria p__Synergistetes c__Synergistia o__Synergistales f__Synergistaceae g__uncultured s__ OTU_9681
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Desulfobacterales f__Desulfobulbaceae g__Desulfobulbus s__ OTU_4039
+k__Bacteria p__Actinobacteria c__Thermoleophilia o__Gaiellales f__BVA77 g__ s__ OTU_4338
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Propionibacteriaceae OTU_1634
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__env.OPS 17 g__ s__ OTU_684
+k__Bacteria p__Actinobacteria c__Acidimicrobiia o__Acidimicrobiales OTU_496
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Nocardioidaceae g__Nocardioides s__ OTU_3941
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhizobiales f__DUNssu044 g__ s__ OTU_4193
+k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__uncultured s__ OTU_9455
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Family XII g__Fusibacter s__ OTU_7842
+k__Bacteria p__Planctomycetes c__Phycisphaerae o__Phycisphaerales f__Phycisphaeraceae g__uncultured s__ OTU_13494
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Chitinophagaceae g__uncultured s__ OTU_1285
+k__Bacteria p__Chloroflexi c__WCHB1-50 o__WCHB1-50 f__WCHB1-50 g__SM1F10 s__ OTU_132
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhizobiales f__Hyphomicrobiaceae g__Hyphomicrobium s__ OTU_10641
+k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Rhodocyclales f__Rhodocyclaceae OTU_236
+k__Bacteria p__Deinococcus-Thermus c__Deinococci o__Thermales f__Thermaceae g__Meiothermus s__ OTU_462
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhizobiales f__Hyphomicrobiaceae g__Hyphomicrobium s__ OTU_161
+k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Carnobacteriaceae g__Trichococcus s__ OTU_13660
+k__Bacteria p__Chlorobi c__Ignavibacteria o__Ignavibacteriales f__PHOS-HE36 g__oca15 s__ OTU_9412
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Myxococcales OTU_7504
+k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Burkholderiales f__Comamonadaceae g__Simplicispira s__ OTU_318
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Family XIII OTU_7070
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhizobiales f__Hyphomicrobiaceae OTU_288
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Myxococcales f__Sandaracinaceae g__Sandaracinus s__ OTU_2415
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Bdellovibrionales f__Bdellovibrionaceae g__OM27 clade s__ OTU_95
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rickettsiales f__Mitochondria g__ s__ OTU_3982
+k__Bacteria p__Verrucomicrobia c__Verrucomicrobiae o__Verrucomicrobiales f__Verrucomicrobiaceae g__uncultured s__ OTU_4278
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Saprospiraceae OTU_2887
+k__Bacteria p__Chloroflexi c__Anaerolineae o__Anaerolineales f__Anaerolineaceae g__uncultured s__ OTU_5684
+k__Bacteria OTU_4220
+k__Bacteria OTU_7051
+k__Bacteria p__Actinobacteria c__Coriobacteriia o__Coriobacteriales f__Coriobacteriaceae g__Collinsella s__ OTU_11398
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhizobiales f__Nordellaceae g__MNG7 s__ OTU_4669
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhodospirillales f__Acetobacteraceae g__Roseomonas s__ OTU_4697
+k__Bacteria p__Chloroflexi c__Anaerolineae o__Anaerolineales f__Anaerolineaceae OTU_6765
+k__Bacteria p__Planctomycetes c__Planctomycetacia o__Planctomycetales f__Planctomycetaceae g__Pirellula s__ OTU_1066
+k__Bacteria p__Planctomycetes c__Planctomycetacia o__Planctomycetales f__Planctomycetaceae g__uncultured s__ OTU_5907
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Clostridiaceae 1 g__Clostridium sensu stricto 1 s__ OTU_4933
+k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Lactobacillaceae g__Lactobacillus s__ OTU_8885
+k__Bacteria p__Chloroflexi c__Caldilineae o__Caldilineales f__Caldilineaceae g__Candidatus Defluviifilum s__ OTU_4226
+k__Bacteria p__Proteobacteria c__TA18 o__ f__ g__ s__ OTU_1821
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Peptostreptococcaceae g__Acetoanaerobium s__ OTU_1794
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__env.OPS 17 g__ s__ OTU_3925
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhodospirillales f__Acetobacteraceae OTU_3353
+k__Bacteria p__GOUTA4 c__ o__ f__ g__ s__ OTU_7163
+k__Bacteria p__Acidobacteria c__Acidobacteria o__Subgroup 6 f__ g__ s__ OTU_541
+k__Bacteria p__Bacteroidetes c__Flavobacteriia o__Flavobacteriales f__Flavobacteriaceae g__Flavobacterium s__ OTU_1521
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rickettsiales f__Holosporaceae g__uncultured s__ OTU_14421
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Saprospiraceae g__uncultured s__ OTU_2972
+k__Bacteria p__Nitrospirae c__Nitrospira o__Nitrospirales f__Nitrospiraceae g__Nitrospira s__sublineage I OTU_8291
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Chitinophagaceae g__uncultured s__ OTU_289
+k__Bacteria p__WCHB1-60 c__ o__ f__ g__ s__ OTU_1306
+k__Bacteria p__Planctomycetes c__Phycisphaerae o__WD2101 soil group f__ g__ s__ OTU_4839
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Propionibacteriaceae g__Propioniciclava s__ OTU_11689
+k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__Porphyromonadaceae g__Parabacteroides s__ OTU_12665
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Saprospiraceae OTU_2085
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Saprospiraceae g__uncultured s__ OTU_448
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Actinomycetales f__Actinomycetaceae g__Actinomyces s__ OTU_6935
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Nocardioidaceae g__Aeromicrobium s__ OTU_190
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Family XI g__uncultured s__ OTU_4458
+k__Bacteria OTU_927
+k__Bacteria p__Chlorobi c__Chlorobia o__Chlorobiales f__Chlorobiaceae g__ s__ OTU_5113
+k__Bacteria p__Bacteroidetes c__Flavobacteriia o__Flavobacteriales f__NS9 marine group g__ s__ OTU_1875
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Clostridiaceae 1 g__Clostridium sensu stricto 6 s__ OTU_9228
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhodospirillales f__Rhodospirillales Incertae Sedis g__Reyranella s__ OTU_1845
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Clostridiaceae 1 g__Proteiniclasticum s__ OTU_6255
+k__Bacteria p__Acidobacteria c__Holophagae o__Subgroup 10 f__ABS-19 g__B1-K1A-105 s__ OTU_1479
+k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotellaceae UCG-004 s__ OTU_14146
+k__Bacteria p__Elusimicrobia c__Elusimicrobia o__Lineage IIb f__ g__ s__ OTU_6507
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Myxococcales f__Haliangiaceae g__Haliangium s__ OTU_7542
+k__Bacteria p__Firmicutes c__Bacilli o__Bacillales f__Bacillaceae g__Ureibacillus s__ OTU_13718
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Oligoflexales f__ g__ s__ OTU_4593
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__Ruminococcus 2 s__ OTU_2343
+k__Bacteria OTU_8708
+k__Bacteria p__SM2F11 c__ o__ f__ g__ s__ OTU_2677
+k__Bacteria p__Actinobacteria c__Acidimicrobiia o__Acidimicrobiales OTU_9665
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Saprospiraceae g__CYCU-0281 s__ OTU_81
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Chitinophagaceae g__Parafilimonas s__ OTU_6422
+k__Bacteria p__Proteobacteria c__TA18 o__ f__ g__ s__ OTU_1612
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Actinomycetales f__Actinomycetaceae g__Actinomyces s__ OTU_3216
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Propionibacteriaceae g__Aestuariimicrobium s__ OTU_9248
+k__Bacteria p__Chloroflexi c__Caldilineae o__Caldilineales f__Caldilineaceae g__uncultured s__ OTU_5187
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__Ruminiclostridium 1 s__ OTU_7882
+k__Bacteria p__Saccharibacteria c__ o__ f__ g__ s__ OTU_1543
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Micrococcales f__Microbacteriaceae g__Diaminobutyricimonas s__ OTU_11775
+k__Bacteria p__Actinobacteria c__Thermoleophilia o__Solirubrobacterales f__480-2 g__K2-78 s__ OTU_233
+k__Bacteria p__Firmicutes c__Erysipelotrichia o__Erysipelotrichales f__Erysipelotrichaceae g__Erysipelatoclostridium s__ OTU_4015
+k__Bacteria p__TM6 c__ o__ f__ g__ s__ OTU_8260
+k__Bacteria p__Actinobacteria c__Acidimicrobiia o__Acidimicrobiales f__Acidimicrobiaceae g__CL500-29 marine group s__ OTU_9548
+k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__Bacteroidaceae g__Bacteroides s__ OTU_5643
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Propionibacteriaceae g__Tessaracoccus s__ OTU_1586
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Corynebacteriales f__Nocardiaceae g__Gordonia s__ OTU_3782
+k__Bacteria p__Actinobacteria c__Coriobacteriia o__Coriobacteriales f__Coriobacteriaceae g__Senegalimassilia s__ OTU_2934
+k__Bacteria p__Armatimonadetes c__ o__ f__ g__ s__ OTU_14570
+k__Bacteria p__Actinobacteria c__Coriobacteriia o__Coriobacteriales f__Coriobacteriaceae g__Atopobium s__ OTU_11781
+k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__Porphyromonadaceae g__Proteiniphilum s__ OTU_3700
+k__Bacteria OTU_6318
+k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Rhodocyclales f__Rhodocyclaceae g__Uliginosibacterium s__ OTU_2148
+k__Bacteria p__Chloroflexi c__WCHB1-50 o__WCHB1-50 f__WCHB1-50 g__WCHB1-50 s__ OTU_2244
+k__Bacteria p__Bacteroidetes c__BSV13 o__ f__ g__ s__ OTU_7867
+k__Bacteria p__Actinobacteria c__Thermoleophilia o__Solirubrobacterales f__480-2 g__K2-78 s__ OTU_14248
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Myxococcales f__bacteriap25 g__ s__ OTU_12704
+k__Bacteria p__Chloroflexi c__Thermomicrobia o__JG30-KF-CM45 f__ g__ s__ OTU_364
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Christensenellaceae g__Christensenellaceae R-7 group s__ OTU_8245
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae OTU_10847
+k__Bacteria p__Acidobacteria c__Holophagae o__Holophagales f__Holophagaceae OTU_1151
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Micrococcales f__Intrasporangiaceae g__Fodinibacter s__ OTU_1998
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhodospirillales f__Rhodospirillaceae g__Defluviicoccus s__cluster I OTU_10321
+k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Burkholderiales f__Comamonadaceae g__Acidovorax s__ OTU_4721
+k__Bacteria p__Verrucomicrobia c__OPB35 soil group o__ f__ g__ s__ OTU_6237
+k__Bacteria p__Saccharibacteria c__Unknown Class o__FW73 OTU_1972
+k__Bacteria p__Elusimicrobia c__Elusimicrobia o__Lineage IIb f__ g__ s__ OTU_11364
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Micrococcales f__Beutenbergiaceae g__Salana s__ OTU_1816
+k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Propionibacteriaceae g__Propionimicrobium s__ OTU_14842
+k__Bacteria p__Fusobacteria c__Fusobacteriia o__Fusobacteriales f__Leptotrichiaceae g__uncultured s__ OTU_6533
+k__Bacteria p__Tenericutes c__Mollicutes o__Mollicutes RF9 f__ g__ s__ OTU_8887
+k__Bacteria p__Chloroflexi c__Caldilineae o__Caldilineales f__Caldilineaceae g__Litorilinea s__ OTU_12690
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Clostridiaceae 1 g__Proteiniclasticum s__ OTU_3097
+k__Bacteria p__Firmicutes c__Erysipelotrichia o__Erysipelotrichales f__Erysipelotrichaceae g__Faecalitalea s__ OTU_3257
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhodospirillales f__Acetobacteraceae g__uncultured s__ OTU_3161
+k__Bacteria p__Actinobacteria c__Thermoleophilia o__Solirubrobacterales f__480-2 g__ s__ OTU_11903
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__Ruminiclostridium 5 s__ OTU_7508
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Oligoflexales f__ g__ s__ OTU_10969
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Oligoflexales f__Oligoflexaceae g__ s__ OTU_1801
+k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Neisseriales f__Neisseriaceae g__Rivicola s__ OTU_3488
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__GR-WP33-30 f__ g__ s__ OTU_933
+k__Bacteria p__Lentisphaerae c__PBS-III-20 o__ f__ g__ s__ OTU_3824
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rickettsiales f__AKIW1012 g__ s__ OTU_777
+k__Bacteria p__TM6 c__ o__ f__ g__ s__ OTU_3169
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__[Eubacterium] coprostanoligenes group s__ OTU_12385
+k__Bacteria p__Armatimonadetes c__ o__ f__ g__ s__ OTU_1496
+k__Bacteria p__Actinobacteria c__Acidimicrobiia o__Acidimicrobiales f__Microthricaceae g__ s__ OTU_11294
+k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Saprospiraceae g__Lewinella s__ OTU_1968
+k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rickettsiales OTU_8832
+k__Bacteria p__Proteobacteria c__Deltaproteobacteria OTU_8652
+k__Bacteria p__Chlorobi c__Chlorobia o__Chlorobiales f__OPB56 g__ s__ OTU_13621
+k__Bacteria p__Microgenomates c__ o__ f__ g__ s__ OTU_3043
+k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae OTU_10760
+k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__Bacteroidaceae g__Bacteroides s__ OTU_14173
+k__Bacteria p__Cyanobacteria c__Chloroplast o__ f__ g__ s__ OTU_10746
+k__Bacteria p__Chloroflexi c__Caldilineae o__Caldilineales f__Caldilineaceae g__uncultured s__ OTU_284
+k__Bacteria p__Saccharibacteria c__ o__ f__ g__ s__ OTU_5049
+k__Bacteria p__Chloroflexi c__Anaerolineae o__Anaerolineales f__Anaerolineaceae g__uncultured s__ OTU_2397
+k__Bacteria p__Planctomycetes c__Planctomycetacia o__Planctomycetales f__Planctomycetaceae g__uncultured s__ OTU_2913
+k__Bacteria p__Bacteroidetes OTU_9512
diff -r 3c3c359d9b85 -r e10b5eebd415 test-data/generate.R
--- a/test-data/generate.R Mon Apr 04 10:22:24 2022 +0000
+++ b/test-data/generate.R Thu Apr 07 14:04:02 2022 +0000
@@ -8,3 +8,19 @@
amp_export_otutable(aalborgwwtps, "AalborgWWTPs.otu")
write.table(aalborgwwtps$tax, file = "AalborgWWTPs.tax", quote = F, sep = "\t", row.names = F)
write.table(aalborgwwtps$metadata, file = "AalborgWWTPs.tsv", quote = F, sep = "\t")
+
+# construct data for merge_ampvis2
+t <- amp_load(otutable = "AalborgWWTPs.otu.csv", metadata = "AalborgWWTPs.tsv", taxonomy = "AalborgWWTPs.tax.tsv", fasta = "AalborgWWTPs.fa", tree = "AalborgWWTPs.nwk")
+d_2010 <- amp_subset_samples(t, Period %in% "2010")
+# 60 samples and 109 OTUs have been filtered
+# Before: 67 samples and 200 OTUs
+# After: 7 samples and 91 OTUs
+d_2011 <- amp_subset_samples(t, Period %in% "2011")
+# 61 samples and 94 OTUs have been filtered
+# Before: 67 samples and 200 OTUs
+# After: 6 samples and 106 OTUs
+
+saveRDS(d_2010, "AalborgWWTPs.2010.rds")
+saveRDS(d_2011, "AalborgWWTPs.2011.rds")
+
+# => merging should give 13 samples