From 4aea797a410b07220c0b940b902764a92457160b Mon Sep 17 00:00:00 2001
From: Adrian Sharma <sharma.adrian@gmail.com>
Date: Fri, 19 Jan 2018 16:38:34 -0500
Subject: [PATCH] Create rich_sparse_otu_table.biom

input file for biom convert format tool
---
 .../rich_sparse_otu_table.biom                | 66 +++++++++++++++++++
 1 file changed, 66 insertions(+)
 create mode 100644 _includes/cwl/19-custom-types/rich_sparse_otu_table.biom

diff --git a/_includes/cwl/19-custom-types/rich_sparse_otu_table.biom b/_includes/cwl/19-custom-types/rich_sparse_otu_table.biom
new file mode 100644
index 00000000..1b9a0e2f
--- /dev/null
+++ b/_includes/cwl/19-custom-types/rich_sparse_otu_table.biom
@@ -0,0 +1,66 @@
+{
+     "id":"w00asdt",
+     "format": "1.0.0",
+     "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": "sparse",
+     "matrix_element_type": "int",
+     "shape": [5, 6], 
+     "data":[[0,2,1],
+             [1,0,5],
+             [1,1,1],
+             [1,3,2],
+             [1,4,3],
+             [1,5,1],
+             [2,2,1],
+             [2,3,4],
+             [2,5,2],
+             [3,0,2],
+             [3,1,1],
+             [3,2,1],
+             [3,5,1],
+             [4,1,1],
+             [4,2,1]
+            ]
+    }