Mercurial > repos > iuc > ampvis2_boxplot
changeset 1:0c069fc2471c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
author | iuc |
---|---|
date | Thu, 07 Apr 2022 14:12:09 +0000 (2022-04-07) |
parents | 43776659edf4 |
children | de03693b75b1 |
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 10:29:47 2022 +0000 +++ b/macros.xml Thu Apr 07 14:12:09 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">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs.tax.tsv Thu Apr 07 14:12:09 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 10:29:47 2022 +0000 +++ b/test-data/generate.R Thu Apr 07 14:12:09 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