changeset 2:d80c0fc14504 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit afc6220b1e5f402f872338bbab440e4a1fe04ccd

--- a/kreport2krona.xml	Mon Feb 13 10:23:39 2023 +0000
+++ b/kreport2krona.xml	Mon Mar 06 21:22:47 2023 +0000
@@ -41,22 +41,27 @@
 ------
 A krona-compatible TEXT file
 
-Example output:
-    --no-intermediate-ranks
-        6298        Unclassified
-        8           k__Bacteria
-        4           k__Bacteria     p_Proteobacteria
-        6           k__Bacteria     p_Proteobacteria    c__Gammaproteobacteria
-        ...
+**Example output:**
+
+``--no-intermediate-ranks``
+
+::
+
+    6298        Unclassified
+    8           k__Bacteria
+    4           k__Bacteria     p_Proteobacteria
+    6           k__Bacteria     p_Proteobacteria    c__Gammaproteobacteria
 
-    --intermediate-ranks
-        6298        Unclassified
-        79          x__root
-        0           x__root     x__cellular_organisms
-        8           x__root     x__cellular organisms   k__Bacteria
-        4           x__root     x__cellular organisms   k__Bacteria     p__Proteobacteria
-        6           x__root     x__cellular organisms   k__Bacteria     p__Proteobacteria   c__Gammaproteobacteria
-        ....
+``--intermediate-ranks``
+
+::
+
+    6298        Unclassified
+    79          x__root
+    0           x__root     x__cellular_organisms
+    8           x__root     x__cellular organisms   k__Bacteria
+    4           x__root     x__cellular organisms   k__Bacteria     p__Proteobacteria
+    6           x__root     x__cellular organisms   k__Bacteria     p__Proteobacteria   c__Gammaproteobacteria
 
     ]]></help>
     <expand macro="citations"/>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpa_output.tabular	Mon Mar 06 21:22:47 2023 +0000
@@ -0,0 +1,215 @@
+k__Eukaryota	756
+k__Eukaryota|k__Metazoa	402
+k__Eukaryota|k__Metazoa|p__Chordata	402
+k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia	402
+k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates	402
+k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae	402
+k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae|g__Homo	402
+k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae|g__Homo|s__Homo_sapiens	402
+k__Eukaryota|k__Fungi	342
+k__Eukaryota|k__Fungi|p__Ascomycota	341
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes	336
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales	336
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae	333
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces	329
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces_cerevisiae	293
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces_paradoxus	15
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces_eubayanus	10
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces|s__Kluyveromyces_marxianus	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Trichomonascaceae	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Trichomonascaceae|g__Sugiyamaella	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Trichomonascaceae|g__Sugiyamaella|s__Sugiyamaella_lignohabitans	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Debaryomycetaceae	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Debaryomycetaceae|g__Candida	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Debaryomycetaceae|g__Candida|s__Candida_dubliniensis	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes	3
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae|g__Neurospora	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae|g__Neurospora|s__Neurospora_crassa	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales|f__Pyriculariaceae	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales|f__Pyriculariaceae|g__Pyricularia	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales|f__Pyriculariaceae|g__Pyricularia|s__Pyricularia_pennisetigena	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus_luchuensis	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Schizosaccharomycetes	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales|f__Schizosaccharomycetaceae	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales|f__Schizosaccharomycetaceae|g__Schizosaccharomyces	1
+k__Eukaryota|k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales|f__Schizosaccharomycetaceae|g__Schizosaccharomyces|s__Schizosaccharomyces_pombe	1
+k__Eukaryota|p__Apicomplexa	5
+k__Eukaryota|p__Apicomplexa|c__Aconoidasida	4
+k__Eukaryota|p__Apicomplexa|c__Aconoidasida|o__Haemosporida	4
+k__Eukaryota|p__Apicomplexa|c__Aconoidasida|o__Haemosporida|f__Plasmodiidae	4
+k__Eukaryota|p__Apicomplexa|c__Aconoidasida|o__Haemosporida|f__Plasmodiidae|g__Plasmodium	4
+k__Eukaryota|p__Apicomplexa|c__Aconoidasida|o__Haemosporida|f__Plasmodiidae|g__Plasmodium|s__Plasmodium_vivax	1
+k__Eukaryota|p__Apicomplexa|c__Aconoidasida|o__Haemosporida|f__Plasmodiidae|g__Plasmodium|s__Plasmodium_malariae	1
+k__Eukaryota|p__Apicomplexa|c__Aconoidasida|o__Haemosporida|f__Plasmodiidae|g__Plasmodium|s__Plasmodium_coatneyi	1
+k__Eukaryota|p__Apicomplexa|c__Aconoidasida|o__Haemosporida|f__Plasmodiidae|g__Plasmodium|s__Plasmodium_chabaudi	1
+k__Eukaryota|p__Apicomplexa|c__Conoidasida	1
+k__Eukaryota|p__Apicomplexa|c__Conoidasida|o__Eucoccidiorida	1
+k__Eukaryota|p__Apicomplexa|c__Conoidasida|o__Eucoccidiorida|f__Cryptosporidiidae	1
+k__Eukaryota|p__Apicomplexa|c__Conoidasida|o__Eucoccidiorida|f__Cryptosporidiidae|g__Cryptosporidium	1
+k__Eukaryota|p__Apicomplexa|c__Conoidasida|o__Eucoccidiorida|f__Cryptosporidiidae|g__Cryptosporidium|s__Cryptosporidium_parvum	1
+k__Eukaryota|p__Evosea	1
+k__Eukaryota|p__Evosea|c__Eumycetozoa	1
+k__Eukaryota|p__Evosea|c__Eumycetozoa|o__Dictyosteliales	1
+k__Eukaryota|p__Evosea|c__Eumycetozoa|o__Dictyosteliales|f__Dictyosteliaceae	1
+k__Eukaryota|p__Evosea|c__Eumycetozoa|o__Dictyosteliales|f__Dictyosteliaceae|g__Dictyostelium	1
+k__Eukaryota|p__Evosea|c__Eumycetozoa|o__Dictyosteliales|f__Dictyosteliaceae|g__Dictyostelium|s__Dictyostelium_discoideum	1
+k__Bacteria	51
+k__Bacteria|p__Firmicutes	17
+k__Bacteria|p__Firmicutes|c__Clostridia	9
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales	9
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae	4
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium	4
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium_sp._MF28	1
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium_pasteurianum	1
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium_carboxidivorans	1
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae	2
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Clostridioides	2
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides_difficile	1
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae	1
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium	1
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium]_hylemonae	1
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae	1
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Monoglobus	1
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Monoglobus|s__Monoglobus_pectinilyticus	1
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales_Family_XIII._Incertae_Sedis	1
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales_Family_XIII._Incertae_Sedis|g__Mogibacterium	1
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales_Family_XIII._Incertae_Sedis|g__Mogibacterium|s__Mogibacterium_pumilum	1
+k__Bacteria|p__Firmicutes|c__Bacilli	8
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales	6
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae	3
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus	2
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Halobacillus	1
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Halobacillus|s__Halobacillus_litoralis	1
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae	2
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus	1
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus_saccharolyticus	1
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus	1
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus|s__Jeotgalicoccus_saudimassiliensis	1
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae	1
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus	1
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus_azoreducens	1
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales	2
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae	1
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus	1
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus_lactis	1
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae	1
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella	1
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella_paramesenteroides	1
+k__Bacteria|p__Tenericutes	2
+k__Bacteria|p__Tenericutes|c__Mollicutes	1
+k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales	1
+k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae	1
+k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma	1
+k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma|s__Mycoplasma_sp._Ms02	1
+k__Bacteria|p__Tenericutes|o__Mycoplasmoidales	1
+k__Bacteria|p__Tenericutes|o__Mycoplasmoidales|f__Metamycoplasmataceae	1
+k__Bacteria|p__Tenericutes|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma	1
+k__Bacteria|p__Tenericutes|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma_phocicerebrale	1
+k__Bacteria|p__Cyanobacteria	1
+k__Bacteria|p__Cyanobacteria|o__Chroococcales	1
+k__Bacteria|p__Cyanobacteria|o__Chroococcales|f__Chroococcaceae	1
+k__Bacteria|p__Cyanobacteria|o__Chroococcales|f__Chroococcaceae|g__Chondrocystis	1
+k__Bacteria|p__Cyanobacteria|o__Chroococcales|f__Chroococcaceae|g__Chondrocystis|s__Chondrocystis_sp._NIES-4102	1
+k__Bacteria|p__Proteobacteria	18
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria	14
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales	6
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae	2
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter_sp._RHBSTW-00599	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae	2
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Candidatus_Erwinia_haradaeae	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Buchnera	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Buchnera|s__Buchnera_aphidicola	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella|s__Rahnella_aquatilis	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus|s__Photorhabdus_asymbiotica	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Thiotrichales	5
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Thiotrichales|f__Francisellaceae	5
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Thiotrichales|f__Francisellaceae|g__Francisella	5
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Thiotrichales|f__Francisellaceae|g__Francisella|s__Francisella_halioticida	5
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|g__Candidatus_Nardonella	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|g__Candidatus_Nardonella|s__endosymbiont_of_Sipalinus_gigas	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio_azureus	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter	1
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter_sp._oral_taxon_513	1
+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria	2
+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales	1
+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae	1
+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus	1
+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus_basilensis	1
+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|g__Candidatus_Kinetoplastibacterium	1
+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|g__Candidatus_Kinetoplastibacterium|s__Candidatus_Kinetoplastibacterium_crithidii	1
+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria	2
+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales	2
+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae	2
+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter	2
+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter_hepaticus	2
+k__Bacteria|p__Bacteroidetes	7
+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia	3
+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales	3
+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Blattabacteriaceae	1
+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Blattabacteriaceae|g__Blattabacterium	1
+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Blattabacteriaceae|g__Blattabacterium|s__Blattabacterium_cuenoti	1
+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae	1
+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Olleya	1
+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae	1
+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium	1
+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium_sp._DH-B6	1
+k__Bacteria|p__Bacteroidetes|c__Bacteroidia	2
+k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales	2
+k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia	1
+k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales	1
+k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae	1
+k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium	1
+k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium_multivorum	1
+k__Bacteria|p__Bacteroidetes|c__Cytophagia	1
+k__Bacteria|p__Bacteroidetes|c__Cytophagia|o__Cytophagales	1
+k__Bacteria|p__Bacteroidetes|c__Cytophagia|o__Cytophagales|f__Flammeovirgaceae	1
+k__Bacteria|p__Bacteroidetes|c__Cytophagia|o__Cytophagales|f__Flammeovirgaceae|g__Flammeovirga	1
+k__Bacteria|p__Bacteroidetes|c__Cytophagia|o__Cytophagales|f__Flammeovirgaceae|g__Flammeovirga|s__Flammeovirga_kamogawensis	1
+k__Bacteria|p__Fusobacteria	2
+k__Bacteria|p__Fusobacteria|c__Fusobacteriia	2
+k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales	2
+k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae	2
+k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium	2
+k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium_nucleatum	1
+k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium_hwasookii	1
+k__Bacteria|p__Spirochaetes	1
+k__Bacteria|p__Spirochaetes|c__Spirochaetia	1
+k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales	1
+k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae	1
+k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira	1
+k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira_hyodysenteriae	1
+k__Archaea	2
+k__Archaea|p__Euryarchaeota	1
+k__Archaea|p__Euryarchaeota|c__Methanomicrobia	1
+k__Archaea|p__Euryarchaeota|c__Methanomicrobia|o__Methanosarcinales	1
+k__Archaea|p__Euryarchaeota|c__Methanomicrobia|o__Methanosarcinales|f__Methanosarcinaceae	1
+k__Archaea|p__Euryarchaeota|c__Methanomicrobia|o__Methanosarcinales|f__Methanosarcinaceae|g__Methanosarcina	1
+k__Archaea|p__Euryarchaeota|c__Methanomicrobia|o__Methanosarcinales|f__Methanosarcinaceae|g__Methanosarcina|s__Methanosarcina_barkeri	1
+k__Archaea|p__Thaumarchaeota	1
+k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria	1
+k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria|o__Nitrososphaerales	1
+k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae	1
+k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae|g__Candidatus_Nitrosocosmicus	1
+k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae|g__Candidatus_Nitrosocosmicus|s__Candidatus_Nitrosocosmicus_franklandus	1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpa_output_intermediate.tabular	Mon Mar 06 21:22:47 2023 +0000
@@ -0,0 +1,298 @@
+x__cellular_organisms	836
+x__cellular_organisms|k__Eukaryota	756
+x__cellular_organisms|k__Eukaryota|x__Opisthokonta	747
+x__cellular_organisms|k__Eukaryota|x__Opisthokonta|k__Metazoa	402
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpa_output_percentages.tabular	Mon Mar 06 21:22:47 2023 +0000
@@ -0,0 +1,215 @@
+k__Eukaryota	56.0
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+k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia	29.78
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+k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae|g__Homo|s__Homo_sapiens	29.78
+k__Eukaryota|k__Fungi	25.33
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