# HG changeset patch # User iuc # Date 1481196497 18000 # Node ID 6273e2721fa33ac6a0dea71cef27748bc36669a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c diff -r 000000000000 -r 6273e2721fa3 macros.xml --- /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 @@ + + 1.0.1 + + + picrust + + + + + predict_metagenomes.py --version | cut -d" " -f3 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1038/nbt.2676 + + + + + diff -r 000000000000 -r 6273e2721fa3 normalize_by_copynumber.xml --- /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 @@ + + OTUs by copy number + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 6273e2721fa3 test-data/16S_13_5_precalculated_minimal.tab --- /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 diff -r 000000000000 -r 6273e2721fa3 test-data/categorize_biom.hdf5 Binary file test-data/categorize_biom.hdf5 has changed diff -r 000000000000 -r 6273e2721fa3 test-data/closed_picked_otus.biom --- /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 diff -r 000000000000 -r 6273e2721fa3 test-data/closed_picked_otus.tab --- /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 diff -r 000000000000 -r 6273e2721fa3 test-data/cog_predicted_metagenomes.L2.biom --- /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 diff -r 000000000000 -r 6273e2721fa3 test-data/custom_trait_table.tab --- /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 diff -r 000000000000 -r 6273e2721fa3 test-data/normalized_otus.biom --- /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 diff -r 000000000000 -r 6273e2721fa3 test-data/normalized_otus.classic --- /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 diff -r 000000000000 -r 6273e2721fa3 test-data/observation_table.biom --- /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 diff -r 000000000000 -r 6273e2721fa3 test-data/otu_table_for_custom_trait_table.biom --- /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 diff -r 000000000000 -r 6273e2721fa3 test-data/predicted_metagenomes.L3.biom --- /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 diff -r 000000000000 -r 6273e2721fa3 test-data/tempout.table --- /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 diff -r 000000000000 -r 6273e2721fa3 tool-data/picrust_precalculated.loc.sample --- /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 +# +# +#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 diff -r 000000000000 -r 6273e2721fa3 tool_data_table_conf.xml.sample --- /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 @@ + + + name, value + +
+