changeset 0:6273e2721fa3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
author iuc
date Thu, 08 Dec 2016 06:28:17 -0500
parents
children 76c040c8b9fc
files macros.xml normalize_by_copynumber.xml test-data/16S_13_5_precalculated_minimal.tab test-data/categorize_biom.hdf5 test-data/closed_picked_otus.biom test-data/closed_picked_otus.tab test-data/cog_predicted_metagenomes.L2.biom test-data/custom_trait_table.tab test-data/normalized_otus.biom test-data/normalized_otus.classic test-data/observation_table.biom test-data/otu_table_for_custom_trait_table.biom test-data/predicted_metagenomes.L3.biom test-data/tempout.table tool-data/picrust_precalculated.loc.sample tool_data_table_conf.xml.sample
diffstat 16 files changed, 240 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,90 @@
+<macros>
+    <token name="@WRAPPER_VERSION@">1.0.1</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.0.1">picrust</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="version_command">
+        <version_command>predict_metagenomes.py --version | cut -d" " -f3 </version_command>
+    </xml>
+
+    <xml name="otu-reference-precalculated">
+        <!-- selection of "gg" picrust parameter reference data file -->
+        <conditional name="gg">
+           <param name="source" type="select" label="Select precalculated file from" help="">
+               <option value="ref">Cached Reference</option>
+               <option value="hist">History</option>
+           </param>
+           <when value="ref">
+               <param name="precalc" type="select" label="Precalculated input marker gene copy number predictions on per-otu basis">
+                   <options from_data_table="picrust_precalculated"/>
+               </param>
+           </when>
+           <when value="hist">
+               <param name="precalc" type="data" format="tabular" label="Precalculated input marker gene copy number predictions on per-otu basis"
+                      help="files may be downloaded from PICRUSt website (see tool help below)" />
+           </when>
+       </conditional>
+    </xml>
+
+    <xml name="biom_format_select">
+        <param name="output_type" type="select" label="Format of the output BIOM file">
+            <option value="json" selected="true">JSON</option>
+            <option value="hdf5">HDF5</option>
+            <option value="tsv">Classic (tab-separated text)</option>
+        </param>
+    </xml>
+
+    <xml name="biom_output">
+        <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs">
+            <change_format>
+                <when input="output_type" value="json" format="json"/>
+                <when input="output_type" value="tsv" format="tabular"/>
+                <when input="output_type" value="hdf5" format="hdf5"/>
+            </change_format>
+        </data>
+    </xml>
+
+    <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[
+        #if $output_type == "json":
+            && biom convert -i tempbiom -o '$out_biom' --to-json
+        #elif $output_type == "tsv":
+            && biom convert -i tempbiom -o '$out_biom' --to-tsv
+        #else
+            && biom convert -i tempbiom -o '$out_biom' --to-hdf5
+        #end if
+    ]]></token>
+
+    <token name="@PICRUST_OVERVIEW@">
+<![CDATA[
+**PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States**
+
+The PICRUSt project aims to support prediction of the unobserved character states in a community of
+organisms from phylogenetic information about the organisms in that community. The primary application
+is to predict gene family abundance (e.g. the metagenome) in environmental DNA samples for which only
+marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative
+bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs.
+
+For more information please visit:
+
+- Picrust Documentation: https://picrust.github.io/picrust/
+- Picrust GitHub: http://picrust.github.com/
+- Picrust Support: https://groups.google.com/d/forum/picrust-users
+
+**Reference Data**
+
+Precalculated files: ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/
+
+]]>
+    </token>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/nbt.2676</citation>
+            <yield/>
+        </citations>
+    </xml>
+
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/normalize_by_copynumber.xml	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,61 @@
+<tool id="picrust_normalize_by_copy_number" name="Normalize" version="@WRAPPER_VERSION@.0">
+    <description>OTUs by copy number</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        normalize_by_copy_number.py
+            -i '$input_data'
+            -o tempbiom
+            -c '$gg.precalc'
+
+            @OUTPUT_CONVERSION_COMMANDS@
+    ]]></command>
+    <inputs>
+        <param name="input_data" type="data" format="tabular,biom1" label="Input file" help="biom file or legacy QIIME OTU table"/>
+        <expand macro="otu-reference-precalculated"/>
+        <expand macro="biom_format_select"/>
+    </inputs>
+    <outputs>
+        <expand macro="biom_output"/>
+    </outputs>
+    <tests>
+        <test> <!-- test with biom input -->
+            <param name="input_data" value="closed_picked_otus.biom"/>
+            <param name="source" value="hist"/>
+            <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
+            <param name="output_type" value="json"/>
+            <output name="out_biom" ftype="json">
+                <assert_contents>
+                    <has_text text="Biological Observation Matrix"/>
+                    <has_text text="generated_by"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test> <!-- test with QIIME input and classic output -->
+            <param name="input_data" value="closed_picked_otus.tab"/>
+            <param name="source" value="hist"/>
+            <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
+            <param name="output_type" value="tsv"/>
+            <output name="out_biom" file="normalized_otus.classic" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+@PICRUST_OVERVIEW@
+
+**Command Documenation**
+
+This module corrects the abundance of each OTU to better reflect the true organism abundance by normalizing by PICRUSt's prediction of 16S copy number for each OTU.
+
+Please ensure that you have properly created your OTU table to be compatible with PICRUSt by following this guide_.
+A sample file can be downloaded here_
+
+.. _guide: http://picrust.github.com/picrust/methods/constructing_reference_otus.html
+.. _here: https://raw.github.com/picrust/picrust/master/tutorials/hmp_mock_16S.tab
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/16S_13_5_precalculated_minimal.tab	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,5 @@
+#OTU_IDs	16S_rRNA_Count
+290426	10.0
+265267	5.0
+248563	4.0
+61102	4.0
\ No newline at end of file
Binary file test-data/categorize_biom.hdf5 has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closed_picked_otus.biom	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,1 @@
+{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "OTU table","generated_by": "BIOM-Format 1.1.2-dev","date": "2013-08-20T16:13:50.386985","matrix_type": "sparse","matrix_element_type": "float","shape": [4, 2],"data": [[0,0,1.0],[1,0,2.0],[2,1,2.0],[3,0,1.0],[3,1,1.0]],"rows": [{"id": "290426", "metadata": null},{"id": "265267", "metadata": null},{"id": "248563", "metadata": null},{"id": "61102", "metadata": null}],"columns": [{"id": "sample1", "metadata": null},{"id": "sample2", "metadata": null}]}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closed_picked_otus.tab	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,6 @@
+# Constructed from biom file
+#OTU ID	sample1	sample2
+290426	1	0
+265267	2	0
+248563	0	2
+61102	1	1
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cog_predicted_metagenomes.L2.biom	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,1 @@
+{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "Gene table","generated_by": "picrust 1.0.0-dev - categorize_by_function","date": "2013-10-10T12:55:15.589322","matrix_type": "sparse","matrix_element_type": "float","shape": [25, 2],"data": [[1,0,2.0],[1,1,2.0],[2,0,275.0],[2,1,128.0],[3,0,74.0],[3,1,18.0],[4,0,577.0],[4,1,233.0],[5,0,231.0],[5,1,50.0],[6,0,540.0],[6,1,144.0],[7,0,218.0],[7,1,93.0],[8,0,196.0],[8,1,96.0],[9,0,473.0],[9,1,142.0],[10,0,566.0],[10,1,216.0],[11,0,368.0],[11,1,110.0],[12,0,353.0],[12,1,121.0],[13,0,103.0],[13,1,72.0],[14,0,213.0],[14,1,73.0],[15,0,323.0],[15,1,111.0],[16,0,100.0],[16,1,55.0],[17,0,747.0],[17,1,251.0],[18,0,500.0],[18,1,95.0],[19,0,326.0],[19,1,166.0],[20,0,134.0],[20,1,58.0],[21,0,154.0],[21,1,34.0]],"rows": [{"id": "[A] RNA processing and modification", "metadata": {"COG_Category": ["INFORMATION STORAGE AND PROCESSING", "[A] RNA processing and modification"]}},{"id": "[B] Chromatin structure and dynamics", "metadata": {"COG_Category": ["INFORMATION STORAGE AND PROCESSING", "[B] Chromatin structure and dynamics"]}},{"id": "[C] Energy production and conversion", "metadata": {"COG_Category": ["METABOLISM", "[C] Energy production and conversion"]}},{"id": "[D] Cell cycle control, cell division, chromosome partitioning", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[D] Cell cycle control, cell division, chromosome partitioning"]}},{"id": "[E] Amino acid transport and metabolism", "metadata": {"COG_Category": ["METABOLISM", "[E] Amino acid transport and metabolism"]}},{"id": "[F] Nucleotide transport and metabolism", "metadata": {"COG_Category": ["METABOLISM", "[F] Nucleotide transport and metabolism"]}},{"id": "[G] Carbohydrate transport and metabolism", "metadata": {"COG_Category": ["METABOLISM", "[G] Carbohydrate transport and metabolism"]}},{"id": "[H] Coenzyme transport and metabolism", "metadata": {"COG_Category": ["METABOLISM", "[H] Coenzyme transport and metabolism"]}},{"id": "[I] Lipid transport and metabolism", "metadata": {"COG_Category": ["METABOLISM", "[I] Lipid transport and metabolism"]}},{"id": "[J] Translation, ribosomal structure and biogenesis", "metadata": {"COG_Category": ["INFORMATION STORAGE AND PROCESSING", "[J] Translation, ribosomal structure and biogenesis"]}},{"id": "[K] Transcription", "metadata": {"COG_Category": ["INFORMATION STORAGE AND PROCESSING", "[K] Transcription"]}},{"id": "[L] Replication, recombination and repair", "metadata": {"COG_Category": ["INFORMATION STORAGE AND PROCESSING", "[L] Replication, recombination and repair"]}},{"id": "[M] Cell wall/membrane/envelope biogenesis", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[M] Cell wall/membrane/envelope biogenesis"]}},{"id": "[N] Cell motility", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[N] Cell motility"]}},{"id": "[O] Post-translational modification, protein turnover, and chaperones", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[O] Post-translational modification, protein turnover, and chaperones"]}},{"id": "[P] Inorganic ion transport and metabolism", "metadata": {"COG_Category": ["METABOLISM", "[P] Inorganic ion transport and metabolism"]}},{"id": "[Q] Secondary metabolites biosynthesis, transport, and catabolism", "metadata": {"COG_Category": ["METABOLISM", "[Q] Secondary metabolites biosynthesis, transport, and catabolism"]}},{"id": "[R] General function prediction only", "metadata": {"COG_Category": ["POORLY CHARACTERIZED", "[R] General function prediction only"]}},{"id": "[S] Function unknown", "metadata": {"COG_Category": ["POORLY CHARACTERIZED", "[S] Function unknown"]}},{"id": "[T] Signal transduction mechanisms", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[T] Signal transduction mechanisms"]}},{"id": "[U] Intracellular trafficking, secretion, and vesicular transport", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[U] Intracellular trafficking, secretion, and vesicular transport"]}},{"id": "[V] Defense mechanisms", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[V] Defense mechanisms"]}},{"id": "[W] Extracellular structures", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[W] Extracellular structures"]}},{"id": "[Y] Nuclear structure", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[Y] Nuclear structure"]}},{"id": "[Z] Cytoskeleton", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[Z] Cytoskeleton"]}}],"columns": [{"id": "staggered", "metadata": null},{"id": "even", "metadata": null}]}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_trait_table.tab	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,5 @@
+#OTU_IDs	trait1	trait2	metadata_NSTI
+A	1.0	2.0	0.0
+C	1.0	1.0	0.0
+B	1.0	0.0	0.0
+D	1.0	1.0	0.7
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/normalized_otus.biom	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,1 @@
+{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "OTU table","generated_by": "BIOM-Format 1.1.2-dev","date": "2013-08-19T13:58:00.733870","matrix_type": "sparse","matrix_element_type": "float","shape": [4, 2],"data": [[0,0,0.090909090909100002],[1,0,2.5],[2,1,0.083333333333299994],[3,0,0.5],[3,1,0.5]],"rows": [{"id": "290426", "metadata": null},{"id": "265267", "metadata": null},{"id": "248563", "metadata": null},{"id": "61102", "metadata": null}],"columns": [{"id": "staggered", "metadata": null},{"id": "even", "metadata": null}]}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/normalized_otus.classic	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,6 @@
+# Constructed from biom file
+#OTU ID	sample1	sample2
+290426	0.1	0.0
+265267	0.4	0.0
+248563	0.0	0.5
+61102	0.25	0.25
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/observation_table.biom	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,1 @@
+{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "OTU table","generated_by": "QIIME 1.6.0","date": "2013-05-16T01:50:26.488550","matrix_type": "sparse","matrix_element_type": "int","shape": [4, 3],"data": [[0,0,1],[1,1,1],[2,2,1],[3,0,1]],"rows": [{"id": "651338519", "metadata": {"taxonomy": ["None"]}},{"id": "644273636", "metadata": {"taxonomy": ["Environmental Information Processing", " Membrane Transport", " Transporters", " K09686"]}},{"id": "644269307", "metadata": {"taxonomy": ["None"]}},{"id": "644228691", "metadata": {"taxonomy": ["None"]}}],"columns": [{"id": "121.PD", "metadata": null},{"id": "124.PD", "metadata": null},{"id": "123.PD", "metadata": null}]}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/otu_table_for_custom_trait_table.biom	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,1 @@
+{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "picrust","date": "2015-03-07T11:40:42.151151","type": "OTU table","matrix_element_type": "float","shape": [3, 4],"data": [[0,0,1.0],[0,1,2.0],[0,2,3.0],[0,3,5.0],[1,0,5.0],[1,1,1.0],[1,3,2.0],[2,2,1.0],[2,3,4.0]],"rows": [{"id": "A", "metadata": null},{"id": "B", "metadata": null},{"id": "C", "metadata": null}],"columns": [{"id": "Sample1", "metadata": {"pH": 7.0}},{"id": "Sample2", "metadata": {"pH": 8.0}},{"id": "Sample3", "metadata": {"pH": 7.0}},{"id": "Sample4", "metadata": {"pH": NaN}}]}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/predicted_metagenomes.L3.biom	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,1 @@
+{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "Gene table","generated_by": "picrust 0.9.1-dev - categorize_by_function","date": "2013-05-27T13:45:53.337575","matrix_type": "sparse","matrix_element_type": "float","shape": [333, 2],"data": 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and neomycin biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Butirosin and neomycin biosynthesis"]}},{"id": "C5-Branched dibasic acid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "C5-Branched dibasic acid metabolism"]}},{"id": "CAM ligands", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "CAM ligands"]}},{"id": "Caffeine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Caffeine metabolism"]}},{"id": "Calcium signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "Calcium signaling pathway"]}},{"id": "Caprolactam degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Caprolactam degradation"]}},{"id": "Carbohydrate digestion and absorption", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Digestive System", "Carbohydrate digestion and absorption"]}},{"id": "Carbohydrate metabolism", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Carbohydrate metabolism"]}},{"id": "Carbon fixation in photosynthetic organisms", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Carbon fixation in photosynthetic organisms"]}},{"id": "Carbon fixation pathways in prokaryotes", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Carbon fixation pathways in prokaryotes"]}},{"id": "Cardiac muscle contraction", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Circulatory System", "Cardiac muscle contraction"]}},{"id": "Carotenoid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Carotenoid biosynthesis"]}},{"id": "Cell adhesion molecules (CAMs)", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "Cell adhesion molecules (CAMs)"]}},{"id": "Cell cycle", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Growth and Death", "Cell cycle"]}},{"id": "Cell cycle - Caulobacter", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Growth and Death", "Cell cycle - Caulobacter"]}},{"id": "Cell cycle - yeast", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Growth and Death", "Cell cycle - yeast"]}},{"id": "Cell division", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Cell division"]}},{"id": "Cell motility and secretion", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Cell motility and secretion"]}},{"id": "Cellular antigens", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "Cellular antigens"]}},{"id": "Chagas disease (American trypanosomiasis)", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Chagas disease (American trypanosomiasis)"]}},{"id": "Chaperones and folding catalysts", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Folding, Sorting and Degradation", "Chaperones and folding catalysts"]}},{"id": "Chloroalkane and chloroalkene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Chloroalkane and chloroalkene degradation"]}},{"id": "Chlorocyclohexane and chlorobenzene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Chlorocyclohexane and chlorobenzene degradation"]}},{"id": "Cholinergic synapse", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Nervous System", "Cholinergic synapse"]}},{"id": "Chromosome", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "Chromosome"]}},{"id": "Chronic myeloid leukemia", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Chronic myeloid leukemia"]}},{"id": "Circadian rhythm - mammal", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Environmental Adaptation", "Circadian rhythm - mammal"]}},{"id": "Circadian rhythm - plant", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Environmental Adaptation", "Circadian rhythm - plant"]}},{"id": "Citrate cycle (TCA cycle)", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Citrate cycle (TCA cycle)"]}},{"id": "Clavulanic acid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Clavulanic acid biosynthesis"]}},{"id": "Colorectal cancer", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Colorectal cancer"]}},{"id": "Complement and coagulation cascades", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "Complement and coagulation cascades"]}},{"id": "Cyanoamino acid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "Cyanoamino acid metabolism"]}},{"id": "Cysteine and methionine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Cysteine and methionine metabolism"]}},{"id": "Cytochrome P450", "metadata": {"KEGG_Pathways": ["Metabolism", "Enzyme Families", "Cytochrome P450"]}},{"id": "Cytokine receptors", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "Cytokine receptors"]}},{"id": "Cytokine-cytokine receptor interaction", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "Cytokine-cytokine receptor interaction"]}},{"id": "Cytoskeleton proteins", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Motility", "Cytoskeleton proteins"]}},{"id": "Cytosolic DNA-sensing pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "Cytosolic DNA-sensing pathway"]}},{"id": "D-Alanine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "D-Alanine metabolism"]}},{"id": "D-Arginine and D-ornithine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "D-Arginine and D-ornithine metabolism"]}},{"id": "D-Glutamine and D-glutamate metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "D-Glutamine and D-glutamate metabolism"]}},{"id": "DNA repair and recombination proteins", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "DNA repair and recombination proteins"]}},{"id": "DNA replication", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "DNA replication"]}},{"id": "DNA replication proteins", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "DNA replication proteins"]}},{"id": "Dilated cardiomyopathy (DCM)", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cardiovascular Diseases", "Dilated cardiomyopathy (DCM)"]}},{"id": "Dioxin degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Dioxin degradation"]}},{"id": "Drug metabolism - cytochrome P450", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Drug metabolism - cytochrome P450"]}},{"id": "Drug metabolism - other enzymes", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Drug metabolism - other enzymes"]}},{"id": "ECM-receptor interaction", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "ECM-receptor interaction"]}},{"id": "Electron transfer carriers", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Electron transfer carriers"]}},{"id": "Endocrine and other factor-regulated calcium reabsorption", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Excretory System", "Endocrine and other factor-regulated calcium reabsorption"]}},{"id": "Endocytosis", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Transport and Catabolism", "Endocytosis"]}},{"id": "Energy metabolism", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Energy metabolism"]}},{"id": "Epithelial cell signaling in Helicobacter pylori infection", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Epithelial cell signaling in Helicobacter pylori infection"]}},{"id": "ErbB signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "ErbB signaling pathway"]}},{"id": "Ether lipid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Ether lipid metabolism"]}},{"id": "Ethylbenzene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Ethylbenzene degradation"]}},{"id": "Fat digestion and absorption", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Digestive System", "Fat digestion and absorption"]}},{"id": "Fatty acid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Fatty acid biosynthesis"]}},{"id": "Fatty acid elongation in mitochondria", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Fatty acid elongation in mitochondria"]}},{"id": "Fatty acid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Fatty acid metabolism"]}},{"id": "Fc epsilon RI signaling pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "Fc epsilon RI signaling pathway"]}},{"id": "Fc gamma R-mediated phagocytosis", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "Fc gamma R-mediated phagocytosis"]}},{"id": "Flagellar assembly", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Motility", "Flagellar assembly"]}},{"id": "Flavone and flavonol biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Flavone and flavonol biosynthesis"]}},{"id": "Flavonoid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Flavonoid biosynthesis"]}},{"id": "Fluorobenzoate degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Fluorobenzoate degradation"]}},{"id": "Focal adhesion", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Communication", "Focal adhesion"]}},{"id": "Folate biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Folate biosynthesis"]}},{"id": "Fructose and mannose metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Fructose and mannose metabolism"]}},{"id": "Function unknown", "metadata": {"KEGG_Pathways": ["Unclassified", "Poorly Characterized", "Function unknown"]}},{"id": "G protein-coupled receptors", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "G protein-coupled receptors"]}},{"id": "GTP-binding proteins", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "GTP-binding proteins"]}},{"id": "Galactose metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Galactose metabolism"]}},{"id": "Gastric acid secretion", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Digestive System", "Gastric acid secretion"]}},{"id": "General function prediction only", "metadata": {"KEGG_Pathways": ["Unclassified", "Poorly Characterized", "General function prediction only"]}},{"id": "Geraniol degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Geraniol degradation"]}},{"id": "Germination", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Germination"]}},{"id": "Glioma", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Glioma"]}},{"id": "Glutamatergic synapse", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Nervous System", "Glutamatergic synapse"]}},{"id": "Glutathione metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "Glutathione metabolism"]}},{"id": "Glycan bindng proteins", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "Glycan bindng proteins"]}},{"id": "Glycan biosynthesis and metabolism", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Glycan biosynthesis and metabolism"]}},{"id": "Glycerolipid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Glycerolipid metabolism"]}},{"id": "Glycerophospholipid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Glycerophospholipid metabolism"]}},{"id": "Glycine, serine and threonine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Glycine, serine and threonine metabolism"]}},{"id": "Glycolysis / Gluconeogenesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Glycolysis / Gluconeogenesis"]}},{"id": "Glycosaminoglycan biosynthesis - chondroitin sulfate", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosaminoglycan biosynthesis - chondroitin sulfate"]}},{"id": "Glycosaminoglycan biosynthesis - heparan sulfate", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosaminoglycan biosynthesis - heparan sulfate"]}},{"id": "Glycosaminoglycan degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosaminoglycan degradation"]}},{"id": "Glycosphingolipid biosynthesis - ganglio series", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosphingolipid biosynthesis - ganglio series"]}},{"id": "Glycosphingolipid biosynthesis - globo series", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosphingolipid biosynthesis - globo series"]}},{"id": "Glycosphingolipid biosynthesis - lacto and neolacto series", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosphingolipid biosynthesis - lacto and neolacto series"]}},{"id": "Glycosylphosphatidylinositol(GPI)-anchor biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosylphosphatidylinositol(GPI)-anchor biosynthesis"]}},{"id": "Glycosyltransferases", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosyltransferases"]}},{"id": "Glyoxylate and dicarboxylate metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Glyoxylate and dicarboxylate metabolism"]}},{"id": "GnRH signaling pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Endocrine System", "GnRH signaling pathway"]}},{"id": "Hedgehog signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "Hedgehog signaling pathway"]}},{"id": "Hematopoietic cell lineage", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "Hematopoietic cell lineage"]}},{"id": "Hepatitis C", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Hepatitis C"]}},{"id": "Histidine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Histidine metabolism"]}},{"id": "Homologous recombination", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "Homologous recombination"]}},{"id": "Huntington's disease", "metadata": {"KEGG_Pathways": ["Human Diseases", "Neurodegenerative Diseases", "Huntington's disease"]}},{"id": "Hypertrophic cardiomyopathy (HCM)", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cardiovascular Diseases", "Hypertrophic cardiomyopathy (HCM)"]}},{"id": "Indole alkaloid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Indole alkaloid biosynthesis"]}},{"id": "Influenza A", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Influenza A"]}},{"id": "Inorganic ion transport and metabolism", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Inorganic ion transport and metabolism"]}},{"id": "Inositol phosphate metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Inositol phosphate metabolism"]}},{"id": "Insulin signaling pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Endocrine System", "Insulin signaling pathway"]}},{"id": "Ion channels", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "Ion channels"]}},{"id": "Isoflavonoid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Isoflavonoid biosynthesis"]}},{"id": "Isoquinoline alkaloid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Isoquinoline alkaloid biosynthesis"]}},{"id": "Leishmaniasis", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Leishmaniasis"]}},{"id": "Leukocyte transendothelial migration", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "Leukocyte transendothelial migration"]}},{"id": "Limonene and pinene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Limonene and pinene degradation"]}},{"id": "Linoleic acid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Linoleic acid metabolism"]}},{"id": "Lipid biosynthesis proteins", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Lipid biosynthesis proteins"]}},{"id": "Lipid metabolism", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Lipid metabolism"]}},{"id": "Lipoic acid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Lipoic acid metabolism"]}},{"id": "Lipopolysaccharide biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Lipopolysaccharide biosynthesis"]}},{"id": "Lipopolysaccharide biosynthesis proteins", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Lipopolysaccharide biosynthesis proteins"]}},{"id": "Long-term depression", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Nervous System", "Long-term depression"]}},{"id": "Long-term potentiation", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Nervous System", "Long-term potentiation"]}},{"id": "Lysine biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Lysine biosynthesis"]}},{"id": "Lysine degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Lysine degradation"]}},{"id": "Lysosome", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Transport and Catabolism", "Lysosome"]}},{"id": "MAPK signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "MAPK signaling pathway"]}},{"id": "MAPK signaling pathway - yeast", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "MAPK signaling pathway - yeast"]}},{"id": "Measles", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Measles"]}},{"id": "Meiosis - yeast", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Growth and Death", "Meiosis - yeast"]}},{"id": "Melanogenesis", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Endocrine System", "Melanogenesis"]}},{"id": "Membrane and intracellular structural molecules", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Membrane and intracellular structural molecules"]}},{"id": "Metabolism of cofactors and vitamins", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Metabolism of cofactors and vitamins"]}},{"id": "Metabolism of xenobiotics by cytochrome P450", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Metabolism of xenobiotics by cytochrome P450"]}},{"id": "Methane metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Methane metabolism"]}},{"id": "Mineral absorption", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Digestive System", "Mineral absorption"]}},{"id": "Mismatch repair", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "Mismatch repair"]}},{"id": "N-Glycan biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "N-Glycan biosynthesis"]}},{"id": "NOD-like receptor signaling pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "NOD-like receptor signaling pathway"]}},{"id": "Naphthalene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Naphthalene degradation"]}},{"id": "Neuroactive ligand-receptor interaction", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "Neuroactive ligand-receptor interaction"]}},{"id": "Neurotrophin signaling pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Nervous System", "Neurotrophin signaling pathway"]}},{"id": "Nicotinate and nicotinamide metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Nicotinate and nicotinamide metabolism"]}},{"id": "Nitrogen metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Nitrogen metabolism"]}},{"id": "Nitrotoluene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Nitrotoluene degradation"]}},{"id": "Non-coding RNAs", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "RNA family", "Non-coding RNAs"]}},{"id": "Non-homologous end-joining", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "Non-homologous end-joining"]}},{"id": "Notch signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "Notch signaling pathway"]}},{"id": "Novobiocin biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Novobiocin biosynthesis"]}},{"id": "Nucleotide excision repair", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "Nucleotide excision repair"]}},{"id": "Nucleotide metabolism", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Nucleotide metabolism"]}},{"id": "Olfactory transduction", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Sensory System", "Olfactory transduction"]}},{"id": "One carbon pool by folate", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "One carbon pool by folate"]}},{"id": "Oocyte meiosis", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Growth and Death", "Oocyte meiosis"]}},{"id": "Other glycan degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Other glycan degradation"]}},{"id": "Other ion-coupled transporters", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Other ion-coupled transporters"]}},{"id": "Other transporters", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Other transporters"]}},{"id": "Other types of O-glycan biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Other types of O-glycan biosynthesis"]}},{"id": "Others", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Others"]}},{"id": "Oxidative phosphorylation", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Oxidative phosphorylation"]}},{"id": "PPAR signaling pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Endocrine System", "PPAR signaling pathway"]}},{"id": "Pancreatic cancer", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Pancreatic cancer"]}},{"id": "Pancreatic secretion", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Digestive System", "Pancreatic secretion"]}},{"id": "Pantothenate and CoA biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Pantothenate and CoA biosynthesis"]}},{"id": "Parkinson's disease", "metadata": {"KEGG_Pathways": ["Human Diseases", "Neurodegenerative Diseases", "Parkinson's disease"]}},{"id": "Pathogenic Escherichia coli infection", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Pathogenic Escherichia coli infection"]}},{"id": "Pathways in cancer", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Pathways in cancer"]}},{"id": "Penicillin and cephalosporin biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Penicillin and cephalosporin biosynthesis"]}},{"id": "Pentose and glucuronate interconversions", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Pentose and glucuronate interconversions"]}},{"id": "Pentose phosphate pathway", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Pentose phosphate pathway"]}},{"id": "Peptidases", "metadata": {"KEGG_Pathways": ["Metabolism", "Enzyme Families", "Peptidases"]}},{"id": "Peptidoglycan biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Peptidoglycan biosynthesis"]}},{"id": "Peroxisome", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Transport and Catabolism", "Peroxisome"]}},{"id": "Pertussis", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Pertussis"]}},{"id": "Phagosome", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Transport and Catabolism", "Phagosome"]}},{"id": "Phenylalanine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Phenylalanine metabolism"]}},{"id": "Phenylalanine, tyrosine and tryptophan biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Phenylalanine, tyrosine and tryptophan biosynthesis"]}},{"id": "Phenylpropanoid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Phenylpropanoid biosynthesis"]}},{"id": "Phosphatidylinositol signaling system", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "Phosphatidylinositol signaling system"]}},{"id": "Phosphonate and phosphinate metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "Phosphonate and phosphinate metabolism"]}},{"id": "Phosphotransferase system (PTS)", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Membrane Transport", "Phosphotransferase system (PTS)"]}},{"id": "Photosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Photosynthesis"]}},{"id": "Photosynthesis - antenna proteins", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Photosynthesis - antenna proteins"]}},{"id": "Photosynthesis proteins", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Photosynthesis proteins"]}},{"id": "Phototransduction", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Sensory System", "Phototransduction"]}},{"id": "Phototransduction - fly", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Sensory System", "Phototransduction - fly"]}},{"id": "Plant-pathogen interaction", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Environmental Adaptation", "Plant-pathogen interaction"]}},{"id": "Polycyclic aromatic hydrocarbon degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Polycyclic aromatic hydrocarbon degradation"]}},{"id": "Polyketide sugar unit biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Polyketide sugar unit biosynthesis"]}},{"id": "Pores ion channels", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Pores ion channels"]}},{"id": "Porphyrin and chlorophyll metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Porphyrin and chlorophyll metabolism"]}},{"id": "Prenyltransferases", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Prenyltransferases"]}},{"id": "Primary bile acid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Primary bile acid biosynthesis"]}},{"id": "Primary immunodeficiency", "metadata": {"KEGG_Pathways": ["Human Diseases", "Immune System Diseases", "Primary immunodeficiency"]}},{"id": "Prion diseases", "metadata": {"KEGG_Pathways": ["Human Diseases", "Neurodegenerative Diseases", "Prion diseases"]}},{"id": "Progesterone-mediated oocyte maturation", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Endocrine System", "Progesterone-mediated oocyte maturation"]}},{"id": "Propanoate metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Propanoate metabolism"]}},{"id": "Prostate cancer", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Prostate cancer"]}},{"id": "Proteasome", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Folding, Sorting and Degradation", "Proteasome"]}},{"id": "Protein digestion and absorption", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Digestive System", "Protein digestion and absorption"]}},{"id": "Protein export", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Folding, Sorting and Degradation", "Protein export"]}},{"id": "Protein folding and associated processing", "metadata": {"KEGG_Pathways": ["Unclassified", "Genetic Information Processing", "Protein folding and associated processing"]}},{"id": "Protein kinases", "metadata": {"KEGG_Pathways": ["Metabolism", "Enzyme Families", "Protein kinases"]}},{"id": "Protein processing in endoplasmic reticulum", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Folding, Sorting and Degradation", "Protein processing in endoplasmic reticulum"]}},{"id": "Proximal tubule bicarbonate reclamation", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Excretory System", "Proximal tubule bicarbonate reclamation"]}},{"id": "Purine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Nucleotide Metabolism", "Purine metabolism"]}},{"id": "Pyrimidine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Nucleotide Metabolism", "Pyrimidine metabolism"]}},{"id": "Pyruvate metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Pyruvate metabolism"]}},{"id": "RIG-I-like receptor signaling pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "RIG-I-like receptor signaling pathway"]}},{"id": "RNA degradation", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Folding, Sorting and Degradation", "RNA degradation"]}},{"id": "RNA polymerase", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Transcription", "RNA polymerase"]}},{"id": "RNA transport", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Translation", "RNA transport"]}},{"id": "Regulation of actin cytoskeleton", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Motility", "Regulation of actin cytoskeleton"]}},{"id": "Renal cell carcinoma", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Renal cell carcinoma"]}},{"id": "Renin-angiotensin system", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Endocrine System", "Renin-angiotensin system"]}},{"id": "Replication, recombination and repair proteins", "metadata": {"KEGG_Pathways": ["Unclassified", "Genetic Information Processing", "Replication, recombination and repair proteins"]}},{"id": "Restriction enzyme", "metadata": {"KEGG_Pathways": ["Unclassified", "Genetic Information Processing", "Restriction enzyme"]}},{"id": "Retinol metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Retinol metabolism"]}},{"id": "Rheumatoid arthritis", "metadata": {"KEGG_Pathways": ["Human Diseases", "Immune System Diseases", "Rheumatoid arthritis"]}},{"id": "Riboflavin metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Riboflavin metabolism"]}},{"id": "Ribosome", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Translation", "Ribosome"]}},{"id": "Ribosome Biogenesis", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Translation", "Ribosome Biogenesis"]}},{"id": "Ribosome biogenesis in eukaryotes", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Translation", "Ribosome biogenesis in eukaryotes"]}},{"id": "Salivary secretion", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Digestive System", "Salivary secretion"]}},{"id": "Secondary bile acid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Secondary bile acid biosynthesis"]}},{"id": "Secretion system", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Membrane Transport", "Secretion system"]}},{"id": "Selenocompound metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "Selenocompound metabolism"]}},{"id": "Sesquiterpenoid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Sesquiterpenoid biosynthesis"]}},{"id": "Shigellosis", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Shigellosis"]}},{"id": "Signal transduction mechanisms", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Signal transduction mechanisms"]}},{"id": "Small cell lung cancer", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Small cell lung cancer"]}},{"id": "Sphingolipid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Sphingolipid metabolism"]}},{"id": "Spliceosome", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Transcription", "Spliceosome"]}},{"id": "Sporulation", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Sporulation"]}},{"id": "Staphylococcus aureus infection", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Staphylococcus aureus infection"]}},{"id": "Starch and sucrose metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Starch and sucrose metabolism"]}},{"id": "Steroid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Steroid biosynthesis"]}},{"id": "Steroid hormone biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Steroid hormone biosynthesis"]}},{"id": "Stilbenoid, diarylheptanoid and gingerol biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Stilbenoid, diarylheptanoid and gingerol biosynthesis"]}},{"id": "Streptomycin biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Streptomycin biosynthesis"]}},{"id": "Styrene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Styrene degradation"]}},{"id": "Sulfur metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Sulfur metabolism"]}},{"id": "Sulfur relay system", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Folding, Sorting and Degradation", "Sulfur relay system"]}},{"id": "Synthesis and degradation of ketone bodies", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Synthesis and degradation of ketone bodies"]}},{"id": "Systemic lupus erythematosus", "metadata": {"KEGG_Pathways": ["Human Diseases", "Immune System Diseases", "Systemic lupus erythematosus"]}},{"id": "TGF-beta signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "TGF-beta signaling pathway"]}},{"id": "Taurine and hypotaurine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "Taurine and hypotaurine metabolism"]}},{"id": "Terpenoid backbone biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Terpenoid backbone biosynthesis"]}},{"id": "Tetracycline biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Tetracycline biosynthesis"]}},{"id": "Thiamine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Thiamine metabolism"]}},{"id": "Tight junction", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Communication", "Tight junction"]}},{"id": "Toluene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Toluene degradation"]}},{"id": "Toxoplasmosis", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Toxoplasmosis"]}},{"id": "Transcription factors", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Transcription", "Transcription factors"]}},{"id": "Transcription machinery", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Transcription", "Transcription machinery"]}},{"id": "Transcription related proteins", "metadata": {"KEGG_Pathways": ["Unclassified", "Genetic Information Processing", "Transcription related proteins"]}},{"id": "Translation factors", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Translation", "Translation factors"]}},{"id": "Translation proteins", "metadata": {"KEGG_Pathways": ["Unclassified", "Genetic Information Processing", "Translation proteins"]}},{"id": "Transporters", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Membrane Transport", "Transporters"]}},{"id": "Tropane, piperidine and pyridine alkaloid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Tropane, piperidine and pyridine alkaloid biosynthesis"]}},{"id": "Tryptophan metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Tryptophan metabolism"]}},{"id": "Tuberculosis", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Tuberculosis"]}},{"id": "Two-component system", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "Two-component system"]}},{"id": "Type I diabetes mellitus", "metadata": {"KEGG_Pathways": ["Human Diseases", "Metabolic Diseases", "Type I diabetes mellitus"]}},{"id": "Type II diabetes mellitus", "metadata": {"KEGG_Pathways": ["Human Diseases", "Metabolic Diseases", "Type II diabetes mellitus"]}},{"id": "Tyrosine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Tyrosine metabolism"]}},{"id": "Ubiquinone and other terpenoid-quinone biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Ubiquinone and other terpenoid-quinone biosynthesis"]}},{"id": "Ubiquitin system", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Folding, Sorting and Degradation", "Ubiquitin system"]}},{"id": "VEGF signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "VEGF signaling pathway"]}},{"id": "Valine, leucine and isoleucine biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Valine, leucine and isoleucine biosynthesis"]}},{"id": "Valine, leucine and isoleucine degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Valine, leucine and isoleucine degradation"]}},{"id": "Various types of N-glycan biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Various types of N-glycan biosynthesis"]}},{"id": "Vascular smooth muscle contraction", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Circulatory System", "Vascular smooth muscle contraction"]}},{"id": "Vasopressin-regulated water reabsorption", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Excretory System", "Vasopressin-regulated water reabsorption"]}},{"id": "Vibrio cholerae infection", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Vibrio cholerae infection"]}},{"id": "Vibrio cholerae pathogenic cycle", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Vibrio cholerae pathogenic cycle"]}},{"id": "Viral myocarditis", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cardiovascular Diseases", "Viral myocarditis"]}},{"id": "Vitamin B6 metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Vitamin B6 metabolism"]}},{"id": "Wnt signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "Wnt signaling pathway"]}},{"id": "Xylene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Xylene degradation"]}},{"id": "Zeatin biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Zeatin biosynthesis"]}},{"id": "alpha-Linolenic acid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "alpha-Linolenic acid metabolism"]}},{"id": "beta-Alanine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "beta-Alanine metabolism"]}},{"id": "beta-Lactam resistance", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "beta-Lactam resistance"]}},{"id": "mRNA surveillance pathway", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Translation", "mRNA surveillance pathway"]}},{"id": "mTOR signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "mTOR signaling pathway"]}},{"id": "p53 signaling pathway", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Growth and Death", "p53 signaling pathway"]}}],"columns": [{"id": "staggered", "metadata": null},{"id": "even", "metadata": null}]}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tempout.table	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,45 @@
+# Constructed from biom file
+#OTU ID	staggered	even	KEGG_Pathways
+Amino Acid Metabolism	28955185.0	45374765.0	Metabolism; Amino Acid Metabolism
+Biosynthesis of Other Secondary Metabolites	1737365.0	2923945.0	Metabolism; Biosynthesis of Other Secondary Metabolites
+Cancers	282088.0	393993.0	Human Diseases; Cancers
+Carbohydrate Metabolism	33779735.0	44900117.0	Metabolism; Carbohydrate Metabolism
+Cardiovascular Diseases	18668.0	2002.0	Human Diseases; Cardiovascular Diseases
+Cell Communication	26.0	21.0	Cellular Processes; Cell Communication
+Cell Growth and Death	1340246.0	1728222.0	Cellular Processes; Cell Growth and Death
+Cell Motility	3332193.0	4325524.0	Cellular Processes; Cell Motility
+Cellular Processes and Signaling	12376427.0	16085447.0	Unclassified; Cellular Processes and Signaling
+Circulatory System	27563.0	109603.0	Organismal Systems; Circulatory System
+Development	0.0	0.0	Organismal Systems; Development
+Digestive System	205590.0	268235.0	Organismal Systems; Digestive System
+Endocrine System	311963.0	901422.0	Organismal Systems; Endocrine System
+Energy Metabolism	16483126.0	22914670.0	Metabolism; Energy Metabolism
+Environmental Adaptation	263572.0	488829.0	Organismal Systems; Environmental Adaptation
+Enzyme Families	5457311.0	7759696.0	Metabolism; Enzyme Families
+Excretory System	36303.0	100424.0	Organismal Systems; Excretory System
+Folding, Sorting and Degradation	6690470.0	9464060.0	Genetic Information Processing; Folding, Sorting and Degradation
+Genetic Information Processing	7466411.0	10678653.0	Unclassified; Genetic Information Processing
+Glycan Biosynthesis and Metabolism	5153604.0	6993096.0	Metabolism; Glycan Biosynthesis and Metabolism
+Immune System	38800.0	75125.0	Organismal Systems; Immune System
+Immune System Diseases	141292.0	225122.0	Human Diseases; Immune System Diseases
+Infectious Diseases	1734917.0	1799045.0	Human Diseases; Infectious Diseases
+Lipid Metabolism	9430513.0	14243639.0	Metabolism; Lipid Metabolism
+Membrane Transport	40619910.0	51257841.0	Environmental Information Processing; Membrane Transport
+Metabolic Diseases	245399.0	327300.0	Human Diseases; Metabolic Diseases
+Metabolism	7818926.0	11548413.0	Unclassified; Metabolism
+Metabolism of Cofactors and Vitamins	13332788.0	18431813.0	Metabolism; Metabolism of Cofactors and Vitamins
+Metabolism of Other Amino Acids	5175074.0	6958034.0	Metabolism; Metabolism of Other Amino Acids
+Metabolism of Terpenoids and Polyketides	5806434.0	9500869.0	Metabolism; Metabolism of Terpenoids and Polyketides
+Nervous System	174485.0	291743.0	Organismal Systems; Nervous System
+Neurodegenerative Diseases	660119.0	1222484.0	Human Diseases; Neurodegenerative Diseases
+Nucleotide Metabolism	11770630.0	16309025.0	Metabolism; Nucleotide Metabolism
+Poorly Characterized	16616064.0	23170781.0	Unclassified; Poorly Characterized
+RNA family	0.0	0.0	Genetic Information Processing; RNA family
+Replication and Repair	23845775.0	31340489.0	Genetic Information Processing; Replication and Repair
+Sensory System	0.0	0.0	Organismal Systems; Sensory System
+Signal Transduction	6054447.0	7820067.0	Environmental Information Processing; Signal Transduction
+Signaling Molecules and Interaction	503602.0	917661.0	Environmental Information Processing; Signaling Molecules and Interaction
+Transcription	7071835.0	8709955.0	Genetic Information Processing; Transcription
+Translation	14940935.0	19978123.0	Genetic Information Processing; Translation
+Transport and Catabolism	585366.0	1330052.0	Cellular Processes; Transport and Catabolism
+Xenobiotics Biodegradation and Metabolism	7799254.0	12542712.0	Metabolism; Xenobiotics Biodegradation and Metabolism
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/picrust_precalculated.loc.sample	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,10 @@
+#This is a sample file distributed with Galaxy.
+#
+# PICRUSt supplied files: ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/
+#
+# files may be in gzipped format or unzipped
+#
+#<dbname>	<file_base>
+#16S 13_5	/path/to/file/16S_13_5_precalculated.tab.gz
+#cog 13_5	/path/to/file/cog_13_5_precalculated.tab
+#ko 13_5	/path/to/file/ko_13_5_precalculated.tab.gz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,6 @@
+<tables>
+    <table name="picrust_precalculated" comment_char="#">
+        <columns>name, value</columns>
+        <file path="tool-data/picrust_precalculated.loc" />
+    </table>
+</tables>