Mercurial > repos > iuc > phyloseq_from_dada2

diff test-data/rich_dense_otu_table.biom @ 2:87064cb77a52 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
author: iuc
date: Sat, 16 Mar 2024 07:55:48 +0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rich_dense_otu_table.biom	Sat Mar 16 07:55:48 2024 +0000
@@ -0,0 +1,56 @@
+{
+     "id":null,
+     "format": "Biological Observation Matrix 1.0.0-dev",
+     "format_url": "http://biom-format.org",
+     "type": "OTU table",
+     "generated_by": "QIIME revision XYZ",
+     "date": "2011-12-19T19:00:00",  
+     "rows":[
+        {"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}},
+        {"id":"GG_OTU_2", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}},
+        {"id":"GG_OTU_3", "metadata":{"taxonomy":["k__Archaea", "p__Euryarchaeota", "c__Methanomicrobia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__"]}},
+        {"id":"GG_OTU_4", "metadata":{"taxonomy":["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Halanaerobiales", "f__Halanaerobiaceae", "g__Halanaerobium", "s__Halanaerobiumsaccharolyticum"]}},
+        {"id":"GG_OTU_5", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}
+        ],  
+     "columns":[
+        {"id":"Sample1", "metadata":{
+                                 "BarcodeSequence":"CGCTTATCGAGA",
+                                 "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
+                                 "BODY_SITE":"gut",
+                                 "Description":"human gut"}},
+        {"id":"Sample2", "metadata":{
+                                 "BarcodeSequence":"CATACCAGTAGC",
+                                 "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
+                                 "BODY_SITE":"gut",
+                                 "Description":"human gut"}},
+        {"id":"Sample3", "metadata":{
+                                 "BarcodeSequence":"CTCTCTACCTGT",
+                                 "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
+                                 "BODY_SITE":"gut",
+                                 "Description":"human gut"}},
+        {"id":"Sample4", "metadata":{
+                                 "BarcodeSequence":"CTCTCGGCCTGT",
+                                 "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
+                                 "BODY_SITE":"skin",
+                                 "Description":"human skin"}},
+        {"id":"Sample5", "metadata":{
+                                 "BarcodeSequence":"CTCTCTACCAAT",
+                                 "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
+                                 "BODY_SITE":"skin",
+                                 "Description":"human skin"}},
+        {"id":"Sample6", "metadata":{
+                                 "BarcodeSequence":"CTAACTACCAAT",
+                                 "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
+                                 "BODY_SITE":"skin",
+                                 "Description":"human skin"}}
+                ],
+     "matrix_type": "dense",
+     "matrix_element_type": "int",
+     "shape": [5,6],
+     "data":  [[0,0,1,0,0,0], 
+               [5,1,0,2,3,1],
+               [0,0,1,4,2,0],
+               [2,1,1,0,0,1],
+               [0,1,1,0,0,0]]
+    }
+