annotate test-data/rich_dense_otu_table.biom @ 1:1feea247d08a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9

{
     "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]]
    }