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changeset 1:be1918c80d9f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
author iuc
date Thu, 07 Apr 2022 13:57:52 +0000
parents f84ec808bee3
children 8569e8d8b712
files macros.xml test-data/AalborgWWTPs.2010.rds test-data/AalborgWWTPs.2011.rds test-data/AalborgWWTPs.tax.tsv test-data/generate.R
diffstat 5 files changed, 220 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Apr 04 10:16:44 2022 +0000
+++ b/macros.xml	Thu Apr 07 13:57:52 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.7.17</token>
+    <token name="@TOOL_VERSION@">2.7.22</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="header">
@@ -22,8 +22,8 @@
         </citations>
     </xml>
 
-    <xml name="rds_input_macro">
-        <param argument="data" type="data" format="ampvis2" label="Ampvis2 RDS dataset" help="Generated with ampvis2: load"/>
+    <xml name="rds_input_macro" token_multiple="false">
+        <param argument="data" type="data" format="ampvis2" multiple="@MULTIPLE@" label="Ampvis2 RDS dataset" help="Generated with ampvis2: load"/>
     </xml>
     
     <xml name="rds_metadata_input_macro" token_metadata_optional="true">
Binary file test-data/AalborgWWTPs.2010.rds has changed
Binary file test-data/AalborgWWTPs.2011.rds has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/AalborgWWTPs.tax.tsv	Thu Apr 07 13:57:52 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
--- a/test-data/generate.R	Mon Apr 04 10:16:44 2022 +0000
+++ b/test-data/generate.R	Thu Apr 07 13:57:52 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