[{"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [10], "output_datasets": [11], "state": "ok", "params": {"cond": "c132!=1 and c132==c136 and c128!=c132", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "NoneFiltering with c136==0 or c136==2, \nkept 95.18% of 7659722 valid lines (7659722 total lines).\n", "peek": 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"individual_columns": [9, 13, 17, 21, 25, 29, 33, 37, 41, 45, 49, 53, 57, 61, 65, 69, 73, 77, 81, 85, 89, 93, 97, 101, 105, 109, 113, 117], "ref": 6, "scaffold": 6, "columns": 137}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [10], "output_datasets": [12], "state": "ok", "params": {"cond": "c128!=1 and c128==c136 and c132!=c136", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "NoneFiltering with c136==0 or c136==2, \nkept 95.18% of 7659722 valid lines (7659722 total lines).\n", "peek": 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pathways\n\nchr1\t3266093\tENSCAFT00000000001\tENSCAFP00000000001\tN\t582\tD\t92.6\t144\t100856150\t3266093chr1\tContig46_chr1_3265165_3266703\t946\tT\tC\t143.0\tchr1\t3266093\tT\t2\t0\t2\t33\t4\t0\t2\t39\t5\t0\t2\t42\t3\t0\t2\t36\t3\t0\t2\t36\t7\t0\t2\t48\t14\t0\t2\t69\t13\t0\t2\t66\t4\t0\t2\t39\t5\t0\t2\t42\t10\t0\t2\t57\t3\t0\t2\n\t36\t6\t0\t2\t45\t6\t0\t2\t45\t6\t0\t2\t45\t5\t0\t2\t42\t3\t0\t2\t36\t1\t0\t2\t30\t0\t0\t-1\t0\t0\t0\t-1\t0\t1\t0\t2\t30\t0\t0\t-1\t0\t0\t0\t-1\t0\t3\t0\t2\t36\t0\t20\t0\t57\t29\t0\t2\t114\t22\t0\t2\t93\t18\t0\t2\t81\tY\t44\t0.373\t0\t0.1639\t104\t0\t2\t69\t51\t20\t1\t114\t18\t0\t2\t81\t3266093chr1\t476153\tcfa00230=Purine metabolism.cfa0\n0500=Starch and sucrose metabolism.cfa00740=Riboflavin metabolism.cfa00760=Nicotinate and nicotinamide metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa01100=Metabolic pathways\n", "update_time": "2013-06-17 04:32:22.063298", "name": "(Method 1) Get Pathways on bear non-synonymous SNPs formatted ABC-GRZ", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/024/dataset_24976.dat", "tags": {}, "deleted": false, "designation": "output", "parent_id": null, "create_time": "2013-06-16 22:37:56.829599", "hid": 27, "annotation": "None", "blurb": "7,162 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 7162, "column_types": ["str", "int", "str", "str", "str", "int", "str", "float", "int", "str", "str", "str", "int", "str", "str", "float", "str", "int", "str", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", 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"2\t1\t1\t0.037\tcfa00780=Biotin metabolism\n\n4\t0.57\t2\t0.029\tcfa00460=Cyanoamino acid metabolism\n\n5\t0.56\t3\t0.016\tcfa00062=Fatty acid elongation\n\n8\t0.5\t4\t0.0054\tcfa00450=Selenocompound metabolism\n\n2\t0.5\t4\t0.17\tcfa00061=Fatty acid biosynthesis\n\n39\t0.49\t6\t1.7E-9\tcfa04512=ECM-receptor interaction\n", "update_time": "2013-06-17 04:32:01.838453", "name": "(Method 1) Rank Pathways on bear non-synonymous SNPs formatted polar", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/024/dataset_24978.dat", "tags": {}, "deleted": false, "designation": "output", "parent_id": null, "create_time": "2013-06-16 22:40:26.369907", "hid": 29, "annotation": "None", "blurb": "241 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 241, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [30], "output_datasets": [32], "state": "ok", "params": {"cond": "c4<=0.05", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "", "peek": "1\t1\t1\t0.18\tcfa00472=D-Arginine and D-ornithine metabolism\n\n7\t0.58\t2\t0.0018\tcfa03450=Non-homologous end-joining\n\n4\t0.57\t3\t0.022\tcfa00460=Cyanoamino acid metabolism\n\n8\t0.5\t4\t0.0031\tcfa00450=Selenocompound metabolism\n\n2\t0.5\t4\t0.15\tcfa00750=Vitamin B6 metabolism\n\n1\t0.5\t4\t0.32\tcfa00780=Biotin metabolism\n", "update_time": "2013-06-17 04:31:45.907472", "name": "(Method 1) Rank Pathways on bear non-synonymous SNPs formatted ABC-GRZ", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/024/dataset_24979.dat", "tags": {}, "deleted": false, "designation": "output", "parent_id": null, "create_time": "2013-06-16 22:40:39.280009", "hid": 30, "annotation": "None", "blurb": "241 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 241, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [23], "output_datasets": [34], "state": "ok", "params": {"cond": "c5.find('ATP')>-1 or c5.find('oxid')>-1 or c5.find('energ')>-1 or c5.find('mitoc')>-1 or c5.find('Oxid')>-1 or c5.find('Energ')>-1 or c5.find('Mitoc')>-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "Filtering with c4<=0.05, \r\nkept 2.46% of 10458 valid lines (10458 total lines).\r\n", "peek": "5\t1\t1\t0.0020\tpolysaccharide binding\n\n5\t1\t1\t0.0020\tanion transmembrane transporter activity\n\n4\t1\t1\t0.0070\tresponse to temperature stimulus\n\n4\t1\t1\t0.0070\tprotein targeting to lysosome\n\n4\t1\t1\t0.0070\tmuscle alpha-actinin binding\n\n4\t1\t1\t0.0070\tequilibrioception\n", "update_time": "2013-06-17 04:33:31.343968", "name": "(Method 1) Rank GO terms on non-synonymous SNPs derived in polar (statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/024/dataset_24972.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-16 22:30:01.474768", "hid": 23, "annotation": "None", "blurb": "257 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 257, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [25], "output_datasets": [36], "state": "ok", "params": {"cond": "c5.find('ATP')>-1 or c5.find('oxid')>-1 or c5.find('energ')>-1 or c5.find('mitoc')>-1 or c5.find('Oxid')>-1 or c5.find('Energ')>-1 or c5.find('Mitoc')>-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "Filtering with c4<=0.05, \r\nkept 2.59% of 10458 valid lines (10458 total lines).\r\n", "peek": "6\t1\t1\t0.00031\tcollagen type IV\n\n5\t1\t1\t0.0012\tleukocyte tethering or rolling\n\n5\t1\t1\t0.0012\tendodeoxyribonuclease activity\n\n4\t1\t1\t0.0045\tvitamin D metabolic process\n\n4\t1\t1\t0.0045\tsingle-stranded DNA specific endodeoxyribonuclease activity\n\n4\t1\t1\t0.0045\tmuscle alpha-actinin binding\n", "update_time": "2013-06-17 04:33:00.870003", "name": "(Method 1) Rank GO terms on non-synonymous SNPs derived in ABC-GRZ (statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/024/dataset_24974.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-16 22:32:29.999705", "hid": 25, "annotation": "None", "blurb": "271 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 271, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [31], "output_datasets": [37], "state": "ok", "params": {"cond": "c5.find('ATP')>-1 or c5.find('oxid')>-1 or c5.find('energ')>-1 or c5.find('mitoc')>-1 or c5.find('Oxid')>-1 or c5.find('Energ')>-1 or c5.find('Mitoc')>-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "Filtering with c4<=0.05, \r\nkept 23.65% of 241 valid lines (241 total lines).\r\n", "peek": "2\t1\t1\t0.037\tcfa00780=Biotin metabolism\n\n4\t0.57\t2\t0.029\tcfa00460=Cyanoamino acid metabolism\n\n5\t0.56\t3\t0.016\tcfa00062=Fatty acid elongation\n\n8\t0.5\t4\t0.0054\tcfa00450=Selenocompound metabolism\n\n39\t0.49\t6\t1.7E-9\tcfa04512=ECM-receptor interaction\n\n20\t0.49\t6\t0.000019\tcfa02010=ABC transporters\n", "update_time": "2013-06-17 04:31:32.008486", "name": "(Method 1) Rank Pathways on bear non-synonymous SNPs formatted polar (statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/024/dataset_24980.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-16 22:41:59.133845", "hid": 31, "annotation": "None", "blurb": "57 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 57, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [32], "output_datasets": [38], "state": "ok", "params": {"cond": "c5.find('ATP')>-1 or c5.find('oxid')>-1 or c5.find('energ')>-1 or c5.find('mitoc')>-1 or c5.find('Oxid')>-1 or c5.find('Energ')>-1 or c5.find('Mitoc')>-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "None", "peek": "7\t0.58\t2\t0.0018\tcfa03450=Non-homologous end-joining\n\n4\t0.57\t3\t0.022\tcfa00460=Cyanoamino acid metabolism\n\n8\t0.5\t4\t0.0031\tcfa00450=Selenocompound metabolism\n\n22\t0.49\t7\t0.0000017\tcfa03460=Fanconi anemia pathway\n\n9\t0.47\t8\t0.0028\tcfa00531=Glycosaminoglycan degradation\n\n8\t0.47\t8\t0.0050\tcfa00511=Other glycan degradation\n", "update_time": "2013-06-17 04:31:18.067683", "name": "(Method 1) Rank Pathways on bear non-synonymous SNPs formatted ABC-GRZ (statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/024/dataset_24981.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-16 22:42:32.789240", "hid": 32, "annotation": "None", "blurb": "54 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 54, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "comp1", "tool_version": "1.0.2", "input_datasets": [15, 43], "output_datasets": [57], "state": "ok", "params": {"input2": {"info": "None", "peek": "Contig137_chr1_3318581_3318883\t163\tT\tC\t999.0\tchr1\t3318736\tT\t5\t0\t2\t42\t6\t0\t2\t45\t2\t0\t2\t33\t2\t0\t2\t33\t3\t0\t2\t36\t18\t0\t2\t81\t19\t0\t2\t84\t20\t0\t2\t87\t19\t0\t2\t84\t1\t0\t2\t30\t16\t0\t2\t75\t8\t0\t2\t51\t17\t0\t2\t78\t7\t0\t2\t48\t12\t0\t2\t63\t4\t0\t2\t39\t2\t0\t2\t33\t1\t0\t2\t30\t5\t0\t2\t42\t0\t0\t-1\t0\t2\t0\t2\t33\t\n1\t0\t2\t30\t3\t0\t2\t36\t0\t0\t-1\t0\t0\t31\t0\t90\t0\t40\t0\t117\t0\t42\t0\t123\t41\t0\t2\t150\tY\t78\t0.175\t2\t1.0000\t173\t0\t2\t87\t0\t113\t0\t123\t41\t0\t2\t150\t3318736chr1\n\nContig167_chr1_3341093_3341273\t155\tA\tG\t999.0\tchr1\t3341248\tG\t0\t0\t-1\t0\t1\t0\t2\t30\t0\t0\t-1\t0\t0\t0\t-1\t0\t0\t0\t-1\t0\t1\t1\t2\t10\t1\t1\t2\t10\t4\t0\t2\t39\t4\t0\t2\t39\t1\t0\t2\t30\t3\t0\t2\t36\t1\t0\t2\t30\t3\t0\t2\t36\t1\t0\t2\t30\t3\t0\t2\t36\t0\t0\t-1\t0\t0\t0\t-1\t0\t0\t0\t-1\t0\t1\t0\t2\t30\t1\t0\t2\t30\t1\t0\t2\t30\t0\t0\t-1\t\n0\t2\t0\t2\t33\t0\t0\t-1\t0\t0\t6\t0\t18\t0\t11\t0\t33\t0\t3\t0\t6\t8\t0\t2\t51\tN\t596\t+99.\t1\t0.8750\t28\t2\t2\t39\t0\t20\t0\t33\t8\t0\t2\t51\t3341248chr1\n\nContig36_chr1_3378709_3378915\t79\tA\tG\t999.0\tchr1\t3378792\tA\t2\t0\t2\t33\t0\t0\t-1\t0\t2\t0\t2\t33\t4\t0\t2\t39\t2\t0\t2\t33\t19\t0\t2\t84\t7\t0\t2\t48\t21\t0\t2\t90\t13\t0\t2\t66\t1\t0\t2\t30\t10\t0\t2\t57\t6\t0\t2\t45\t11\t0\t2\t60\t8\t0\t2\t51\t8\t0\t2\t51\t1\t0\t2\t30\t0\t0\t-1\t0\t3\t0\t2\t36\t3\t0\t2\t36\t1\t0\t2\t30\t1\t0\t2\t30\t0\t0\t\n-1\t0\t1\t0\t2\t30\t0\t0\t-1\t0\t0\t20\t0\t57\t0\t17\t0\t48\t0\t25\t0\t53\t0\t27\t0\t81\tN\t45\t1.560\t3\t1.0000\t124\t0\t2\t90\t0\t62\t0\t57\t0\t27\t0\t81\t3378792chr1\n", "update_time": "2013-06-17 04:39:15.787813", "name": "(Method 2) Polar and ABC-GRZ have a different fixed allele formatted", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/019/dataset_19725.dat", "tags": {}, "deleted": false, "designation": null, "parent_id": null, "create_time": "2013-06-17 04:25:59.581400", "hid": 43, "annotation": "None", "blurb": "~960,000 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": null, "column_types": ["str", "int", "str", "str", "float", "str", "int", "str", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", 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"parent_id": null, "create_time": "2013-06-17 04:42:31.483902", "hid": 57, "annotation": "None", "blurb": "7,635 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 7635, "column_types": ["str", "int", "str", "str", "str", "int", "str", "float", "int", "str", "str"], "columns": 11}}}}, {"tool_id": "toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_rank_terms/1.0.0", "tool_version": "1.0.0", "input_datasets": [58, 19], "output_datasets": [59], "state": "ok", "params": {"input2": {"info": "uploaded tabular file", "peek": 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05:20:28.923533", "name": "(Method 2) Polyphen prediction on Genes with fixed different alleles in Polar and ABC-GRZ bears", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/020/dataset_20086.dat", "tags": {}, "deleted": false, "designation": null, "parent_id": null, "create_time": "2013-06-17 05:20:28.807175", "hid": 65, "annotation": null, "blurb": "7,635 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 7635, "column_types": ["str", "int", "str", "str", "str", "int", "str", "float", "int", "str", "str", "str", "str", "str"], "columns": 14}}}}, {"tool_id": "toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_rank_terms/1.0.0", "tool_version": "1.0.0", "input_datasets": [66, 19], "output_datasets": [67], "state": "ok", "params": {"input2": {"info": "uploaded tabular file", "peek": "76\tENSCAFT00000000001\tchr1\t-\t3251711\t3321555\t3252000\t3321555\t24\t3251711,3254074,3255805,3256770,3261442,3263132,3266078,3267859,3268674,3270092,3271373,3273173,3275526,3277853,3278236,3279203,3280378,3281502,3283470,3285512,3286450,3287395,3289282,3321438,\n\t3252171,3254237,3255938,3256851,3261572,3263347,3266237,3267947,3268744,3270220,3271405,3273305,3275635,3277926,3278302,3279313,3280498,3281582,3283568,3285573,3286576,3287512,3289355,3321555,\t0\tENSCAFG00000000001\tcmpl\tincmpl\t0,2,1,1,0,1,1,0,2,0,1,1,0,2,2\n,0,0,1,2,1,1,1,0,0,\tENPP1\tENSCAFT00000000001\tENSCAFP00000000001\t100856150\t3'-phosphoadenosine 5'-phosphosulfate metabolic process.ATP binding.bone remodeling.cell surface.cellular phosphate ion homeostasis.cellular response to insulin stimulus.extracellula\nr space.generation of precursor metabolites and energy.inorganic diphosphate transport.insulin receptor binding.negative regulation of cell growth.negative regulation of fat cell differentiation.negative regulation of glucose import.negative regulation of \nglycogen biosynthetic process.negative regulation of insulin receptor signaling pathway.negative regulation of ossification.negative regulation of protein autophosphorylation.nucleoside triphosphate catabolic process.nucleoside-triphosphate diphosphatase a\nctivity.nucleotide diphosphatase activity.phosphate-containing compound metabolic process.plasma membrane.protein binding.protein homodimerization activity.sequestering of triglyceride\n", "update_time": "2013-06-17 04:41:26.980002", "name": "bear genes + GO", "extension": "interval", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/019/dataset_19731.dat", "tags": {}, "deleted": false, "designation": null, "parent_id": null, "create_time": "2013-06-16 22:22:50.568828", "hid": 19, "annotation": "None", "blurb": "19,305 regions", "metadata": {"chromCol": 3, "column_names": null, "nameCol": 2, "comment_lines": null, "endCol": 6, "dbkey": "canFam2", "strandCol": 4, "startCol": 5, "data_lines": 19305, "column_types": ["int", "str", "str", "str", "int", "int", "int", "int", "int", "list", "list", "int", "str", "str", "str", "list", "str", "str", "str", "str", "str"], "columns": 21}}, "input1": {"info": "Filtering with c14.find('damaging')>-1, \r\nkept 7.58% of 7635 valid lines (7635 total lines).\r\n", "peek": "chr1\t101020385\tENSCAFT00000003500\tENSCAFP00000003246\tC\t523\tR\t86.7\t1079\t476357\t101020385chr1\t476357\tN\tdamaging\n\nchr1\t102877196\tENSCAFT00000003748\tENSCAFP00000003466\tT\t210\tA\t90.3\t83\tU\t102877196chr1\tU\tN\tdamaging\n\nchr30\t10462254\tENSCAFT00000014399\tENSCAFP00000013316\tQ\t1156\tE\t88.1\t184\t100856190\t10462254chr30\t487491\tcfa00562=Inositol phosphate metabolism.cfa01100=Metabolic pathways.cfa04020=Calcium signaling pathway.cfa04062=Chemokine signaling pathway.cfa04070=Phosph\natidylinositol signaling system.cfa04270=Vascular smooth muscle contraction.cfa04310=Wnt signaling pathway.cfa04540=Gap junction.cfa04720=Long-term potentiation.cfa04724=Glutamatergic synapse.cfa04725=Cholinergic synapse.cfa04728=Dopaminergic synapse.cfa04\n730=Long-term depression.cfa04912=GnRH signaling pathway.cfa04916=Melanogenesis.cfa04961=Endocrine and other factor-regulated calcium reabsorption.cfa04970=Salivary secretion.cfa04971=Gastric acid secretion.cfa04972=Pancreatic secretion.cfa05010=Alzheimer'\ns disease.cfa05016=Huntington's disease.cfa05142=Chagas disease (American trypanosomiasis).cfa05143=African trypanosomiasis.cfa05146=Amoebiasis\tdamaging\n", "update_time": "2013-06-17 05:21:54.324021", "name": "(Method 2) Polyphen Damaging prediction on Genes with fixed different alleles in Polar and ABC-GRZ bears", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25001.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-17 05:21:25.082350", "hid": 66, "annotation": "None", "blurb": "579 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 579, "column_types": ["str", "int", "str", "str", "str", "int", "str", "float", "int", "str", "str", "str", "str", "str"], "columns": 14}}, "t_col2": "2", "t_col1": "3", "dbkey": "canFam2", "g_col2": "21", "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len"}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [67], "output_datasets": [68], "state": "ok", "params": {"cond": "c4<=0.05", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "", "peek": "2\t1\t1\t0.00083\tendoplasmic reticulum tubular network organization\n\n2\t1\t1\t0.00083\tATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity\n\n1\t1\t1\t0.029\tzymogen granule membrane\n\n1\t1\t1\t0.029\tvitelline membrane formation\n\n1\t1\t1\t0.029\tvitamin metabolic process\n\n1\t1\t1\t0.029\tvitamin E biosynthetic process\n", "update_time": "2013-06-17 05:24:04.750668", "name": "(Method 2) Rank GO terms Polyphen Damaging prediction on Genes with fixed different alleles in Polar and ABC-GRZ bears", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25002.dat", "tags": {}, "deleted": false, "designation": "output", "parent_id": null, "create_time": "2013-06-17 05:22:50.958855", "hid": 67, "annotation": "None", "blurb": "10,458 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 10458, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [42], "output_datasets": [43], "state": "ok", "params": {"cond": "c136==0 or c136==2", "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "None", "peek": 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"update_time": "2013-03-05 23:02:39.803999", "name": "c136 = Genotype black", "extension": "gd_snp", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/019/dataset_19722.dat", "tags": {}, "deleted": false, "designation": "output", "parent_id": null, "create_time": "2013-03-05 22:58:57.407716", "hid": 42, "annotation": "", "blurb": "7,659,722 lines", "metadata": {"rPos": 7, "column_names": ["scaf", "pos", "A", "B", "qual", "ref", "rpos", "rnuc", "1A", "1B", "1G", "1Q", "2A", "2B", "2G", "2Q", "3A", "3B", "3G", "3Q", "4A", "4B", "4G", "4Q", "5A", "5B", "5G", "5Q", "6A", "6B", "6G", "6Q", "7A", "7B", "7G", "7Q", "8A", "8B", "8G", "8Q", "9A", "9B", "9G", "9Q", "10A", "10B", "10G", "10Q", "11A", "11B", "11G", "11Q", "12A", "12B", "12G", "12Q", "13A", "13B", "13G", "13Q", "14A", "14B", "14G", "14Q", "15A", "15B", "15G", "15Q", "16A", "16B", "16G", "16Q", "17A", "17B", "17G", "17Q", "18A", "18B", "18G", "18Q", "19A", "19B", "19G", "19Q", "20A", "20B", "20G", "20Q", "21A", "21B", "21G", "21Q", "22A", "22B", "22G", "22Q", "23A", "23B", "23G", "23Q", "24A", "24B", "24G", "24Q", "25A", "25B", "25G", "25Q", "26A", "26B", "26G", "26Q", "27A", "27B", "27G", "27Q", "28A", "28B", "28G", "28Q", "pair", "dist", "prim", "rflp"], "comment_metadata": {"rPos": 7, "column_names": ["scaf", "pos", "A", "B", "qual", "ref", "rpos", "rnuc", "1A", "1B", "1G", "1Q", "2A", "2B", "2G", "2Q", "3A", "3B", "3G", "3Q", "4A", "4B", "4G", "4Q", "5A", "5B", "5G", "5Q", "6A", "6B", "6G", "6Q", "7A", "7B", "7G", "7Q", "8A", "8B", "8G", "8Q", "9A", "9B", "9G", "9Q", "10A", "10B", "10G", "10Q", "11A", "11B", "11G", "11Q", "12A", "12B", "12G", "12Q", "13A", "13B", "13G", "13Q", "14A", "14B", "14G", "14Q", "15A", "15B", "15G", "15Q", "16A", "16B", "16G", "16Q", "17A", "17B", "17G", "17Q", "18A", "18B", "18G", "18Q", "19A", "19B", "19G", "19Q", "20A", "20B", "20G", "20Q", "21A", "21B", "21G", "21Q", "22A", "22B", "22G", "22Q", 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"individual_columns": [9, 13, 17, 21, 25, 29, 33, 37, 41, 45, 49, 53, 57, 61, 65, 69, 73, 77, 81, 85, 89, 93, 97, 101, 105, 109, 113, 117], "ref": 6, "scaffold": 6, "columns": 137}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [43], "output_datasets": [44], "state": "ok", "params": {"cond": "(c128==2 and c132==0) or (c128==0 and c132==2)", "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "NoneFiltering with c136==0 or c136==2, \nkept 95.18% of 7659722 valid lines (7659722 total lines).\n", "peek": 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"update_time": "2013-06-17 04:34:42.467126", "name": "(Method 1) non-synonymous SNPs derived in ABC-GRZ formatted", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/024/dataset_24968.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-16 22:17:25.455963", "hid": 18, "annotation": "None", "blurb": "7,162 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 7162, "column_types": ["str", "int", "str", "str", "str", "int", "str", "float", "int", "str", "str", "str", "int", "str", "str", "float", "str", "int", "str", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", "int", 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"chr1\t101020385\tENSCAFT00000003500\tENSCAFP00000003246\tC\t523\tR\t86.7\t1079\t476357\t101020385chr1\t476357\tN\tdamaging\t101020385chr1\n\nchr1\t102877196\tENSCAFT00000003748\tENSCAFP00000003466\tT\t210\tA\t90.3\t83\tU\t102877196chr1\tU\tN\tdamaging\t102877196chr1\n\nchr30\t10462254\tENSCAFT00000014399\tENSCAFP00000013316\tQ\t1156\tE\t88.1\t184\t100856190\t10462254chr30\t487491\tcfa00562=Inositol phosphate metabolism.cfa01100=Metabolic pathways.cfa04020=Calcium signaling pathway.cfa04062=Chemokine signaling pathway.cfa04070=Phosph\natidylinositol signaling system.cfa04270=Vascular smooth muscle contraction.cfa04310=Wnt signaling pathway.cfa04540=Gap junction.cfa04720=Long-term potentiation.cfa04724=Glutamatergic synapse.cfa04725=Cholinergic synapse.cfa04728=Dopaminergic synapse.cfa04\n730=Long-term depression.cfa04912=GnRH signaling pathway.cfa04916=Melanogenesis.cfa04961=Endocrine and other factor-regulated calcium reabsorption.cfa04970=Salivary secretion.cfa04971=Gastric acid 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"chr1\t102877196\tENSCAFT00000003748\tENSCAFP00000003466\tT\t210\tA\t90.3\t83\tU\t102877196chr1\tU\tN\tdamaging\t102877196chr1\n\nchr13\t10623946\tENSCAFT00000001063\tENSCAFP00000000975\tR\t21\tC\t92.3\t614\t100856177\t10623946chr13\t481999\tN\tdamaging\t10623946chr13\n\nchr1\t112367856\tENSCAFT00000006973\tENSCAFP00000006455\tG\t461\tS\t92.3\t252\t476429\t112367856chr1\t476429\tN\tdamaging\t112367856chr1\n\nchr1\t112824747\tENSCAFT00000007105\tENSCAFP00000006579\tE\t584\tG\t95.2\t117\t476434\t112824747chr1\t476434\tN\tdamaging\t112824747chr1\n\nchr1\t115898804\tENSCAFT00000008166\tENSCAFP00000007564\tG\t103\tA\t94.5\t152\t476453\t115898804chr1\t476453\tN\tdamaging\t115898804chr1\n\nchr28\t11855084\tENSCAFT00000013202\tENSCAFP00000012217\tI\t1047\tM\t93.7\t623\t100686806\t11855084chr28\tU\tN\tdamaging\t11855084chr28\n", "update_time": "2013-06-17 05:43:51.724659", "name": "(Method 2) Polyphen Damaging prediction on Genes with fixed different alleles in Polar and ABC-GRZ bears formatted derived in ABC-GRZ", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25009.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-17 05:43:31.640891", "hid": 74, "annotation": "None", "blurb": "170 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 170, "column_types": ["str", "int", "str", "str", "str", "int", "str", "float", "int", "str", "str", "str", "str", "str", "str"], "columns": 15}}, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2"}}, {"tool_id": "toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_calc_freq/1.1.0", "tool_version": "1.1.0", "input_datasets": [83], "output_datasets": [85], "state": "ok", "params": {"kgene": "16", "output_format": "a", "kpath": "17", "dbkey": "canFam2", "input": {"info": "", "peek": "chr1\t101020385\tENSCAFT00000003500\tENSCAFP00000003246\tC\t523\tR\t86.7\t1079\t476357\t101020385chr1\t476357\tN\tdamaging\t101020385chr1\t476357\tN\n\nchr30\t10462254\tENSCAFT00000014399\tENSCAFP00000013316\tQ\t1156\tE\t88.1\t184\t100856190\t10462254chr30\t487491\tcfa00562=Inositol phosphate metabolism.cfa01100=Metabolic pathways.cfa04020=Calcium signaling pathway.cfa04062=Chemokine signaling pathway.cfa04070=Phosph\natidylinositol signaling system.cfa04270=Vascular smooth muscle contraction.cfa04310=Wnt signaling pathway.cfa04540=Gap junction.cfa04720=Long-term potentiation.cfa04724=Glutamatergic synapse.cfa04725=Cholinergic synapse.cfa04728=Dopaminergic synapse.cfa04\n730=Long-term depression.cfa04912=GnRH signaling pathway.cfa04916=Melanogenesis.cfa04961=Endocrine and other factor-regulated calcium reabsorption.cfa04970=Salivary secretion.cfa04971=Gastric acid secretion.cfa04972=Pancreatic secretion.cfa05010=Alzheimer'\ns disease.cfa05016=Huntington's 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"annotation": "None", "blurb": "409 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 409, "column_types": ["str", "int", "str", "str", "str", "int", "str", "float", "int", "str", "str", "str", "str", "str", "str", "str", "str"], "columns": 17}}, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len"}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [85], "output_datasets": [86], "state": "ok", "params": {"cond": "c4<=0.05", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "", "peek": "1\t0.11\t1\t0.11\tcfa00062=Fatty acid elongation\n\n1\t0.091\t2\t0.14\tcfa00790=Folate biosynthesis\n\n1\t0.083\t3\t0.15\tcfa00740=Riboflavin metabolism\n\n3\t0.081\t4\t0.013\tcfa04973=Carbohydrate digestion and absorption\n\n2\t0.08\t5\t0.043\tcfa00534=Glycosaminoglycan biosynthesis - 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"2013-06-17 06:04:53.223853", "name": "(Method 2) Get Pathways on Polyphen Damaging prediction on Genes with fixed different alleles in Polar and ABC-GRZ bears formatted derived in ABC-GRZ", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25019.dat", "tags": {}, "deleted": false, "designation": "output", "parent_id": null, "create_time": "2013-06-17 06:04:37.342518", "hid": 84, "annotation": "None", "blurb": "170 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 170, "column_types": ["str", "int", "str", "str", "str", "int", "str", "float", "int", "str", "str", "str", "str", "str", "str", "str", "str"], "columns": 17}}, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len"}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [87], "output_datasets": [88], "state": "ok", "params": {"cond": "c4<=0.05", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "", "peek": "2\t0.15\t1\t0.0020\tcfa00900=Terpenoid backbone biosynthesis\n\n1\t0.12\t2\t0.040\tcfa00072=Synthesis and degradation of ketone bodies\n\n1\t0.083\t3\t0.059\tcfa03450=Non-homologous end-joining\n\n1\t0.059\t4\t0.083\tcfa04614=Renin-angiotensin system\n\n3\t0.045\t5\t0.0049\tcfa04920=Adipocytokine signaling pathway\n\n2\t0.043\t6\t0.024\tcfa00520=Amino sugar and nucleotide sugar metabolism\n", "update_time": "2013-06-17 06:09:04.328913", "name": "(Method 2) Rank Pathways on Polyphen Damaging prediction on Genes with fixed different alleles in Polar and ABC-GRZ bears formatted derived in ABC-GRZ", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25022.dat", 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"ENSCAFT00000000145\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.00131550132389\t1e-15\t1.31550132389e+12\t1.14734428626\t0.251239919815\n\nENSCAFT00000000160\t1e-15\t0.0018668335712\t5.35666390098e-13\t-1.9653816263\t0.0493700596902\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.0013049155097\t1e-15\t1.3049155097e+12\t1.6436426387\t0.100250536931\n\nENSCAFT00000000338\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.000765696850581\t1e-15\t7.65696850581e+11\t1.15481076415\t0.248168384725\n\nENSCAFT00000000358\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.000572792390611\t1e-15\t5.72792390611e+11\t1.16257830489\t0.245000965471\n\nENSCAFT00000000386\t0.000864428852358\t0.00234833851348\t0.368102318893\t-1.04093091214\t0.297907883956\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.00086405539511\t1e-15\t8.6405539511e+11\t1.16939360546\t0.242245458491\n\nENSCAFT00000000403\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.000831485672749\t1e-15\t8.31485672749e+11\t1.13843723692\t0.254938257162\n", "update_time": "2013-06-17 23:49:12.364535", "name": "(Method 3A) coding SNPs fixed Polar and ABC-GRZ KaKs>1 in polar", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25147.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-17 23:48:08.760619", "hid": 90, "annotation": "None", "blurb": "721 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 721, "column_types": ["str", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float"], "columns": 16}}, "t_col2": "2", "t_col1": "1", "dbkey": "canFam2", "g_col2": "21", "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len"}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [92], "output_datasets": [93], "state": "ok", "params": {"cond": "c4<=0.05", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "None", "peek": "2\t1\t1\t0.0019\tpeptidyl-lysine trimethylation\n\n2\t1\t1\t0.0019\tcellular response to potassium ion\n\n1\t1\t1\t0.044\tzymogen granule membrane\n\n1\t1\t1\t0.044\tvitelline membrane formation\n\n1\t1\t1\t0.044\tvitamin metabolic process\n\n1\t1\t1\t0.044\tvitamin E biosynthetic process\n", "update_time": "2013-06-17 23:52:11.570658", "name": "(Method 3A) Rank Terms on coding SNPs fixed Polar and ABC-GRZ KaKs>1 in polar", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25149.dat", "tags": {}, "deleted": false, "designation": "output", "parent_id": null, "create_time": "2013-06-17 23:51:33.014667", "hid": 92, "annotation": "None", "blurb": "10,458 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 10458, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_rank_terms/1.0.0", "tool_version": "1.0.0", "input_datasets": [91, 19], "output_datasets": [94], "state": "ok", "params": {"input2": {"info": "uploaded tabular file", "peek": "76\tENSCAFT00000000001\tchr1\t-\t3251711\t3321555\t3252000\t3321555\t24\t3251711,3254074,3255805,3256770,3261442,3263132,3266078,3267859,3268674,3270092,3271373,3273173,3275526,3277853,3278236,3279203,3280378,3281502,3283470,3285512,3286450,3287395,3289282,3321438,\n\t3252171,3254237,3255938,3256851,3261572,3263347,3266237,3267947,3268744,3270220,3271405,3273305,3275635,3277926,3278302,3279313,3280498,3281582,3283568,3285573,3286576,3287512,3289355,3321555,\t0\tENSCAFG00000000001\tcmpl\tincmpl\t0,2,1,1,0,1,1,0,2,0,1,1,0,2,2\n,0,0,1,2,1,1,1,0,0,\tENPP1\tENSCAFT00000000001\tENSCAFP00000000001\t100856150\t3'-phosphoadenosine 5'-phosphosulfate metabolic process.ATP binding.bone remodeling.cell surface.cellular phosphate ion homeostasis.cellular response to insulin stimulus.extracellula\nr space.generation of precursor metabolites and energy.inorganic diphosphate transport.insulin receptor binding.negative regulation of cell growth.negative regulation of fat cell differentiation.negative regulation of glucose import.negative regulation of \nglycogen biosynthetic process.negative regulation of insulin receptor signaling pathway.negative regulation of ossification.negative regulation of protein autophosphorylation.nucleoside triphosphate catabolic process.nucleoside-triphosphate diphosphatase a\nctivity.nucleotide diphosphatase activity.phosphate-containing compound metabolic process.plasma membrane.protein binding.protein homodimerization activity.sequestering of triglyceride\n", "update_time": "2013-06-17 04:41:26.980002", "name": "bear genes + GO", "extension": "interval", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/019/dataset_19731.dat", "tags": {}, "deleted": false, "designation": null, "parent_id": null, "create_time": "2013-06-16 22:22:50.568828", "hid": 19, "annotation": "None", "blurb": "19,305 regions", "metadata": {"chromCol": 3, "column_names": null, "nameCol": 2, "comment_lines": null, "endCol": 6, "dbkey": "canFam2", "strandCol": 4, "startCol": 5, "data_lines": 19305, "column_types": ["int", "str", "str", "str", "int", "int", "int", "int", "int", "list", "list", "int", "str", "str", "str", "list", "str", "str", "str", "str", "str"], "columns": 21}}, "input1": {"info": "Filtering with c4>1.0, \r\nkept 10.28% of 4154 valid lines (4154 total lines).\r\nSkipped 1 invalid line(s) starting at line #1: \"ENSEMBL code\tdn_ABC+GRZ\tds_ABC+GRZ\tdn/ds_ABC+GRZ\tt-val_ABC+GRZ\tp_ABC+GRZ\tdn_black\tds_black\tdn/ds_black\tt-val_black\tp_black\tdn_pol", "peek": "ENSCAFT00000000131\t0.000546697062932\t1e-15\t5.46697062932e+11\t1.14156023122\t0.253637270251\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\n\nENSCAFT00000000213\t0.00216606648756\t1e-15\t2.16606648756e+12\t1.16133518909\t0.245505925784\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t0.00644472279212\t1.55165711894e-13\t-1.99890791877\t0.0456182932232\n\nENSCAFT00000000220\t0.00022680022853\t1e-15\t2.2680022853e+11\t1.14758743611\t0.251139203957\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t0.00143163966162\t6.98499787905e-13\t-2.88150368309\t0.00395782316588\n\nENSCAFT00000000295\t9.5797675441e-05\t1e-15\t95797675441.0\t1.14157879781\t0.253629585688\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t0.000316539176422\t3.15916661976e-12\t-2.07488603452\t0.0379970499696\n\nENSCAFT00000000337\t0.00168800183788\t1e-15\t1.68800183788e+12\t1.57550990071\t0.115139313552\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\n\nENSCAFT00000000400\t0.00108303267918\t1e-15\t1.08303267918e+12\t1.17308396069\t0.240762577086\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\n", "update_time": "2013-06-17 23:50:20.698514", "name": "(Method 3A) coding SNPs fixed Polar and ABC-GRZ KaKs>1 in ABC-GRZ", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25148.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-17 23:50:07.199378", "hid": 91, "annotation": "None", "blurb": "427 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 427, "column_types": ["str", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float"], "columns": 16}}, "t_col2": "2", "t_col1": "1", "dbkey": "canFam2", "g_col2": "21", "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len"}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [94], "output_datasets": [95], "state": "ok", "params": {"cond": "c4<=0.05", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "", "peek": "2\t1\t1\t0.00059\tnuclear migration along microfilament\n\n1\t1\t1\t0.024\ttyrosine 3-monooxygenase activity\n\n1\t1\t1\t0.024\ttRNA aminoacylation for mitochondrial protein translation\n\n1\t1\t1\t0.024\tsteroid hormone receptor complex assembly\n\n1\t1\t1\t0.024\tspindle assembly checkpoint\n\n1\t1\t1\t0.024\tsour taste receptor activity\n", "update_time": "2013-06-17 23:55:31.592210", "name": "(Method 3A) Rank Terms on coding SNPs fixed Polar and ABC-GRZ KaKs>1 in ABC-GRZ", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25151.dat", "tags": {}, "deleted": false, "designation": "output", "parent_id": null, "create_time": "2013-06-17 23:55:10.546016", "hid": 94, "annotation": "None", "blurb": "10,458 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 10458, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_new_oscar/1.0.0", "tool_version": "1.0.0", "input_datasets": [90], "output_datasets": [96], "state": "ok", "params": {"ensembl_col": "1", "input": {"info": "Filtering with c14>1.0, \r\nkept 17.36% of 4154 valid lines (4154 total lines).\r\nSkipped 1 invalid line(s) starting at line #1: \"ENSEMBL code\tdn_ABC+GRZ\tds_ABC+GRZ\tdn/ds_ABC+GRZ\tt-val_ABC+GRZ\tp_ABC+GRZ\tdn_black\tds_black\tdn/ds_black\tt-val_black\tp_black\tdn_po", "peek": "ENSCAFT00000000145\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.00131550132389\t1e-15\t1.31550132389e+12\t1.14734428626\t0.251239919815\n\nENSCAFT00000000160\t1e-15\t0.0018668335712\t5.35666390098e-13\t-1.9653816263\t0.0493700596902\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.0013049155097\t1e-15\t1.3049155097e+12\t1.6436426387\t0.100250536931\n\nENSCAFT00000000338\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.000765696850581\t1e-15\t7.65696850581e+11\t1.15481076415\t0.248168384725\n\nENSCAFT00000000358\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.000572792390611\t1e-15\t5.72792390611e+11\t1.16257830489\t0.245000965471\n\nENSCAFT00000000386\t0.000864428852358\t0.00234833851348\t0.368102318893\t-1.04093091214\t0.297907883956\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.00086405539511\t1e-15\t8.6405539511e+11\t1.16939360546\t0.242245458491\n\nENSCAFT00000000403\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.000831485672749\t1e-15\t8.31485672749e+11\t1.13843723692\t0.254938257162\n", "update_time": "2013-06-17 23:49:12.364535", "name": "(Method 3A) coding SNPs fixed Polar and ABC-GRZ KaKs>1 in polar", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25147.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-17 23:48:08.760619", "hid": 90, "annotation": "None", "blurb": "721 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 721, "column_types": ["str", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float"], "columns": 16}}, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2"}}, {"tool_id": "toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_new_oscar/1.0.0", "tool_version": "1.0.0", "input_datasets": [91], "output_datasets": [97], "state": "ok", "params": {"ensembl_col": "1", "input": {"info": "Filtering with c4>1.0, \r\nkept 10.28% of 4154 valid lines (4154 total lines).\r\nSkipped 1 invalid line(s) starting at line #1: \"ENSEMBL code\tdn_ABC+GRZ\tds_ABC+GRZ\tdn/ds_ABC+GRZ\tt-val_ABC+GRZ\tp_ABC+GRZ\tdn_black\tds_black\tdn/ds_black\tt-val_black\tp_black\tdn_pol", "peek": "ENSCAFT00000000131\t0.000546697062932\t1e-15\t5.46697062932e+11\t1.14156023122\t0.253637270251\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\n\nENSCAFT00000000213\t0.00216606648756\t1e-15\t2.16606648756e+12\t1.16133518909\t0.245505925784\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t0.00644472279212\t1.55165711894e-13\t-1.99890791877\t0.0456182932232\n\nENSCAFT00000000220\t0.00022680022853\t1e-15\t2.2680022853e+11\t1.14758743611\t0.251139203957\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t0.00143163966162\t6.98499787905e-13\t-2.88150368309\t0.00395782316588\n\nENSCAFT00000000295\t9.5797675441e-05\t1e-15\t95797675441.0\t1.14157879781\t0.253629585688\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t0.000316539176422\t3.15916661976e-12\t-2.07488603452\t0.0379970499696\n\nENSCAFT00000000337\t0.00168800183788\t1e-15\t1.68800183788e+12\t1.57550990071\t0.115139313552\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\n\nENSCAFT00000000400\t0.00108303267918\t1e-15\t1.08303267918e+12\t1.17308396069\t0.240762577086\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\n", "update_time": "2013-06-17 23:50:20.698514", "name": "(Method 3A) coding SNPs fixed Polar and ABC-GRZ KaKs>1 in ABC-GRZ", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25148.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-17 23:50:07.199378", "hid": 91, "annotation": "None", "blurb": "427 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 427, "column_types": ["str", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float"], "columns": 16}}, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2"}}, {"tool_id": "toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_calc_freq/1.1.0", "tool_version": "1.1.0", "input_datasets": [96], "output_datasets": [98], "state": "ok", "params": {"kgene": "17", "output_format": "a", "kpath": "18", "dbkey": "canFam2", "input": {"info": "", "peek": "ENSCAFT00000000145\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.00131550132389\t1e-15\t1.31550132389e+12\t1.14734428626\t0.251239919815\t483961\tcfa04080=Neuroactive ligand-receptor interaction\n\nENSCAFT00000000160\t1e-15\t0.0018668335712\t5.35666390098e-13\t-1.9653816263\t0.0493700596902\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.0013049155097\t1e-15\t1.3049155097e+12\t1.6436426387\t0.100250536931\t610160\tN\n\nENSCAFT00000000338\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.000765696850581\t1e-15\t7.65696850581e+11\t1.15481076415\t0.248168384725\t483994\tN\n\nENSCAFT00000000358\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.000572792390611\t1e-15\t5.72792390611e+11\t1.16257830489\t0.245000965471\t474413\tN\n\nENSCAFT00000000386\t0.000864428852358\t0.00234833851348\t0.368102318893\t-1.04093091214\t0.297907883956\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.00086405539511\t1e-15\t8.6405539511e+11\t1.16939360546\t0.242245458491\tU\tN\n\nENSCAFT00000000403\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\t0.000831485672749\t1e-15\t8.31485672749e+11\t1.13843723692\t0.254938257162\t484002\tcfa04060=Cytokine-cytokine receptor interaction.cfa04630=Jak-STAT signaling pathway\n", "update_time": "2013-06-18 00:01:53.008594", "name": "(Method 3A) Get Pathways on coding SNPs fixed Polar and ABC-GRZ KaKs>1 in polar", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25153.dat", "tags": {}, "deleted": false, "designation": "output", "parent_id": null, "create_time": "2013-06-17 23:57:45.883998", "hid": 96, "annotation": "None", "blurb": "721 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 721, "column_types": ["str", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "str", "str"], "columns": 18}}, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len"}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [98], "output_datasets": [99], "state": "ok", "params": {"cond": "c4<=0.05", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "", "peek": "1\t0.33\t1\t0.076\tcfa00300=Lysine biosynthesis\n\n3\t0.12\t2\t0.030\tcfa03440=Homologous recombination\n\n3\t0.12\t2\t0.027\tcfa00650=Butanoate metabolism\n\n3\t0.12\t2\t0.027\tcfa00534=Glycosaminoglycan biosynthesis - heparan sulfate\n\n2\t0.12\t2\t0.064\tcfa00120=Primary bile acid biosynthesis\n\n1\t0.12\t2\t0.19\tcfa00072=Synthesis and degradation of ketone bodies\n", "update_time": "2013-06-18 00:03:44.054793", "name": "(Method 3A) Rank Pathways on coding SNPs fixed Polar and ABC-GRZ KaKs>1 in polar", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25155.dat", "tags": {}, "deleted": false, "designation": "output", "parent_id": null, "create_time": "2013-06-18 00:03:13.998760", "hid": 98, "annotation": "None", "blurb": "241 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 241, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_calc_freq/1.1.0", "tool_version": "1.1.0", "input_datasets": [97], "output_datasets": [100], "state": "ok", "params": {"kgene": "17", "output_format": "a", "kpath": "18", "dbkey": "canFam2", "input": {"info": "None", "peek": "ENSCAFT00000000131\t0.000546697062932\t1e-15\t5.46697062932e+11\t1.14156023122\t0.253637270251\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\t474393\tcfa00561=Glycerolipid metabolism.cfa00564=Glycerophospholipid metabolism.cfa01100=Metabolic pathways.cfa04070=P\nhosphatidylinositol signaling system\n\nENSCAFT00000000213\t0.00216606648756\t1e-15\t2.16606648756e+12\t1.16133518909\t0.245505925784\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t0.00644472279212\t1.55165711894e-13\t-1.99890791877\t0.0456182932232\t481113\tN\n\nENSCAFT00000000220\t0.00022680022853\t1e-15\t2.2680022853e+11\t1.14758743611\t0.251139203957\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t0.00143163966162\t6.98499787905e-13\t-2.88150368309\t0.00395782316588\t481116\tN\n\nENSCAFT00000000295\t9.5797675441e-05\t1e-15\t95797675441.0\t1.14157879781\t0.253629585688\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t0.000316539176422\t3.15916661976e-12\t-2.07488603452\t0.0379970499696\tU\tN\n\nENSCAFT00000000337\t0.00168800183788\t1e-15\t1.68800183788e+12\t1.57550990071\t0.115139313552\t1e-15\t1e-15\t1.0\t0.0\t1.0\t1e-15\t1e-15\t1.0\t0.0\t1.0\t474638\tN\n", "update_time": "2013-06-18 00:02:32.834266", "name": "(Method 3A) Get Pathways on coding SNPs fixed Polar and ABC-GRZ KaKs>1 in ABC-GRZ", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25154.dat", "tags": {}, "deleted": false, "designation": "output", "parent_id": null, "create_time": "2013-06-18 00:02:15.630008", "hid": 97, "annotation": "None", "blurb": "427 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 427, "column_types": ["str", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "float", "str", "str"], "columns": 18}}, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len"}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [100], "output_datasets": [101], "state": "ok", "params": {"cond": "c4<=0.05", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "", "peek": "4\t0.21\t1\t0.00022\tcfa01040=Biosynthesis of unsaturated fatty acids\n\n2\t0.15\t2\t0.018\tcfa00900=Terpenoid backbone biosynthesis\n\n2\t0.12\t3\t0.030\tcfa04614=Renin-angiotensin system\n\n1\t0.12\t3\t0.12\tcfa00072=Synthesis and degradation of ketone bodies\n\n3\t0.094\t5\t0.015\tcfa04744=Phototransduction\n\n1\t0.091\t6\t0.16\tcfa00790=Folate biosynthesis\n", "update_time": "2013-06-18 00:05:28.506757", "name": "(Method 3A) Rank Pathways on coding SNPs fixed Polar and ABC-GRZ KaKs>1 in ABC-GRZ", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25157.dat", "tags": {}, "deleted": false, "designation": "output", "parent_id": null, "create_time": "2013-06-18 00:05:03.898433", "hid": 100, "annotation": "None", "blurb": "241 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 241, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [93], "output_datasets": [102], "state": "ok", "params": {"cond": "(c5.find('ATP')>-1 or c5.find('oxid')>-1 or c5.find('energ')>-1 or c5.find('mitoc')>-1 or c5.find('Oxid')>-1 or c5.find('Energ')>-1 or c5.find('Mitoc')>-1) and c5.find('oxidative')==-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "Filtering with c4<=0.05, \r\nkept 2.29% of 10458 valid lines (10458 total lines).\r\n", "peek": "2\t1\t1\t0.0019\tpeptidyl-lysine trimethylation\n\n2\t1\t1\t0.0019\tcellular response to potassium ion\n\n1\t1\t1\t0.044\tzymogen granule membrane\n\n1\t1\t1\t0.044\tvitelline membrane formation\n\n1\t1\t1\t0.044\tvitamin metabolic process\n\n1\t1\t1\t0.044\tvitamin E biosynthetic process\n", "update_time": "2013-06-17 23:53:11.113042", "name": "(Method 3A) Rank Terms on coding SNPs fixed Polar and ABC-GRZ KaKs>1 in polar (statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25150.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-17 23:52:52.075361", "hid": 93, "annotation": "None", "blurb": "240 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 240, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [95], "output_datasets": [104], "state": "ok", "params": {"cond": "(c5.find('ATP')>-1 or c5.find('oxid')>-1 or c5.find('energ')>-1 or c5.find('mitoc')>-1 or c5.find('Oxid')>-1 or c5.find('Energ')>-1 or c5.find('Mitoc')>-1) and c5.find('oxidative')==-1 and c5.find('oxidase')==-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "Filtering with c4<=0.05, \r\nkept 2.62% of 10458 valid lines (10458 total lines).\r\n", "peek": "2\t1\t1\t0.00059\tnuclear migration along microfilament\n\n1\t1\t1\t0.024\ttyrosine 3-monooxygenase activity\n\n1\t1\t1\t0.024\ttRNA aminoacylation for mitochondrial protein translation\n\n1\t1\t1\t0.024\tsteroid hormone receptor complex assembly\n\n1\t1\t1\t0.024\tspindle assembly checkpoint\n\n1\t1\t1\t0.024\tsour taste receptor activity\n", "update_time": "2013-06-17 23:56:06.817026", "name": "(Method 3A) Rank Terms on coding SNPs fixed Polar and ABC-GRZ KaKs>1 in ABC-GRZ (statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25152.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-17 23:55:48.279523", "hid": 95, "annotation": "None", "blurb": "274 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 274, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [99], "output_datasets": [105], "state": "ok", "params": {"cond": "(c5.find('ATP')>-1 or c5.find('oxid')>-1 or c5.find('energ')>-1 or c5.find('mitoc')>-1 or c5.find('Oxid')>-1 or c5.find('Energ')>-1 or c5.find('Mitoc')>-1) and c5.find('oxidative')==-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "Filtering with c4<=0.05, \r\nkept 7.47% of 241 valid lines (241 total lines).\r\n", "peek": "3\t0.12\t2\t0.030\tcfa03440=Homologous recombination\n\n3\t0.12\t2\t0.027\tcfa00650=Butanoate metabolism\n\n3\t0.12\t2\t0.027\tcfa00534=Glycosaminoglycan biosynthesis - heparan sulfate\n\n4\t0.098\t9\t0.022\tcfa02010=ABC transporters\n\n7\t0.097\t10\t0.0028\tcfa03320=PPAR signaling pathway\n\n6\t0.095\t11\t0.0061\tcfa04976=Bile secretion\n", "update_time": "2013-06-18 00:04:15.564385", "name": "(Method 3A) Rank Pathways on coding SNPs fixed Polar and ABC-GRZ KaKs>1 in polar (statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25156.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-18 00:03:59.406937", "hid": 99, "annotation": "None", "blurb": "18 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 18, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [101], "output_datasets": [106], "state": "ok", "params": {"cond": "(c5.find('ATP')>-1 or c5.find('oxid')>-1 or c5.find('energ')>-1 or c5.find('mitoc')>-1 or c5.find('Oxid')>-1 or c5.find('Energ')>-1 or c5.find('Mitoc')>-1) and c5.find('oxidative')==-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "Filtering with c4<=0.05, \r\nkept 6.22% of 241 valid lines (241 total lines).\r\n", "peek": "4\t0.21\t1\t0.00022\tcfa01040=Biosynthesis of unsaturated fatty acids\n\n2\t0.15\t2\t0.018\tcfa00900=Terpenoid backbone biosynthesis\n\n2\t0.12\t3\t0.030\tcfa04614=Renin-angiotensin system\n\n3\t0.094\t5\t0.015\tcfa04744=Phototransduction\n\n6\t0.071\t8\t0.0027\tcfa05410=Hypertrophic cardiomyopathy (HCM)\n\n5\t0.066\t10\t0.0081\tcfa04146=Peroxisome\n", "update_time": "2013-06-18 00:06:01.540550", "name": "(Method 3A) Rank Pathways on coding SNPs fixed Polar and ABC-GRZ KaKs>1 in ABC-GRZ (statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25158.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-18 00:05:44.860801", "hid": 101, "annotation": "None", "blurb": "15 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 15, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "upload1", "tool_version": "1.1.3", "input_datasets": [], "output_datasets": [114], "state": "ok", "params": {"files": [{"NAME": "", "file_data": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/tmp/upload_file_data_bDoI6P", "space_to_tab": null, "url_paste": "None", "__index__": 0, "ftp_files": null}], "paramfile": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/tmp/tmpWiwX0e", "file_type": "auto", "files_metadata": {"file_type": "auto", "__current_case__": 19}, "async_datasets": "30164", "dbkey": "canFam2"}}, {"tool_id": "upload1", "tool_version": "1.1.3", "input_datasets": [], "output_datasets": [115], "state": "ok", "params": {"files": [{"NAME": "", "file_data": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/tmp/upload_file_data_9TQIIF", "space_to_tab": null, "url_paste": "None", "__index__": 0, "ftp_files": null}], "paramfile": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/tmp/tmpq68WHD", "file_type": "auto", "files_metadata": {"file_type": "auto", "__current_case__": 19}, "async_datasets": "30165", "dbkey": "canFam2"}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [114], "output_datasets": [123], "state": "ok", "params": {"cond": "c9.find('polar')>-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "uploaded tabular file", "peek": "polar_ABC+GRZ\tBile secretion\t18\t265298562743.0\t0.435046133126\t89.0\t0.009706903976\tENSCAFT00000003704.ENSCAFT00000003971.ENSCAFT00000004976.ENSCAFT00000006552.ENSCAFT00000007465.ENSCAFT00000008769.ENSCAFT00000011373.ENSCAFT00000015149.ENSCAFT00000015776.ENS\nCAFT00000019177.ENSCAFT00000019466.ENSCAFT00000019757.ENSCAFT00000020561.ENSCAFT00000021332.ENSCAFT00000027259.ENSCAFT00000027704.ENSCAFT00000029367.ENSCAFT00000037977\tpolar\n\npolar_ABC+GRZ\tCell cycle\t19\t132919410090.0\t0.759699050046\t90.5\t0.00379852992534\tENSCAFT00000001725.ENSCAFT00000001862.ENSCAFT00000003425.ENSCAFT00000003463.ENSCAFT00000004945.ENSCAFT00000005562.ENSCAFT00000010616.ENSCAFT00000010664.ENSCAFT00000011883.ENSCA\nFT00000014969.ENSCAFT00000016879.ENSCAFT00000018932.ENSCAFT00000021002.ENSCAFT00000023166.ENSCAFT00000025560.ENSCAFT00000026465.ENSCAFT00000030508.ENSCAFT00000030570.ENSCAFT00000030976\tpolar\n\npolar_ABC+GRZ\tHepatitis C\t16\t123721615870.0\t0.645352706277\t75.5\t0.022045853716\tENSCAFT00000000897.ENSCAFT00000006305.ENSCAFT00000010257.ENSCAFT00000014017.ENSCAFT00000014032.ENSCAFT00000014194.ENSCAFT00000014202.ENSCAFT00000015231.ENSCAFT00000017863.ENSCAF\nT00000024017.ENSCAFT00000026465.ENSCAFT00000027550.ENSCAFT00000027678.ENSCAFT00000029177.ENSCAFT00000031062.ENSCAFT00000039509\tpolar\n", "update_time": "2013-06-18 16:42:55.024389", "name": "(Method 3B) Pathways with average KaKs polar and ABC-GRZ (UMannW statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25175.dat", "tags": {}, "deleted": false, "designation": null, "parent_id": null, "create_time": "2013-06-18 16:39:52.666294", "hid": 114, "annotation": "None", "blurb": "10 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 10, "column_types": ["str", "str", "int", "float", "float", "float", "float", "str", "str"], "columns": 9}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [114], "output_datasets": [124], "state": "ok", "params": {"cond": "c9.find('ABC-GRZ')>-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "uploaded tabular file", "peek": "polar_ABC+GRZ\tBile secretion\t18\t265298562743.0\t0.435046133126\t89.0\t0.009706903976\tENSCAFT00000003704.ENSCAFT00000003971.ENSCAFT00000004976.ENSCAFT00000006552.ENSCAFT00000007465.ENSCAFT00000008769.ENSCAFT00000011373.ENSCAFT00000015149.ENSCAFT00000015776.ENS\nCAFT00000019177.ENSCAFT00000019466.ENSCAFT00000019757.ENSCAFT00000020561.ENSCAFT00000021332.ENSCAFT00000027259.ENSCAFT00000027704.ENSCAFT00000029367.ENSCAFT00000037977\tpolar\n\npolar_ABC+GRZ\tCell cycle\t19\t132919410090.0\t0.759699050046\t90.5\t0.00379852992534\tENSCAFT00000001725.ENSCAFT00000001862.ENSCAFT00000003425.ENSCAFT00000003463.ENSCAFT00000004945.ENSCAFT00000005562.ENSCAFT00000010616.ENSCAFT00000010664.ENSCAFT00000011883.ENSCA\nFT00000014969.ENSCAFT00000016879.ENSCAFT00000018932.ENSCAFT00000021002.ENSCAFT00000023166.ENSCAFT00000025560.ENSCAFT00000026465.ENSCAFT00000030508.ENSCAFT00000030570.ENSCAFT00000030976\tpolar\n\npolar_ABC+GRZ\tHepatitis C\t16\t123721615870.0\t0.645352706277\t75.5\t0.022045853716\tENSCAFT00000000897.ENSCAFT00000006305.ENSCAFT00000010257.ENSCAFT00000014017.ENSCAFT00000014032.ENSCAFT00000014194.ENSCAFT00000014202.ENSCAFT00000015231.ENSCAFT00000017863.ENSCAF\nT00000024017.ENSCAFT00000026465.ENSCAFT00000027550.ENSCAFT00000027678.ENSCAFT00000029177.ENSCAFT00000031062.ENSCAFT00000039509\tpolar\n", "update_time": "2013-06-18 16:42:55.024389", "name": "(Method 3B) Pathways with average KaKs polar and ABC-GRZ (UMannW statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25175.dat", "tags": {}, "deleted": false, "designation": null, "parent_id": null, "create_time": "2013-06-18 16:39:52.666294", "hid": 114, "annotation": "None", "blurb": "10 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 10, "column_types": ["str", "str", "int", "float", "float", "float", "float", "str", "str"], "columns": 9}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [123], "output_datasets": [125], "state": "ok", "params": {"cond": "c2.find('ATP')>-1 or c2.find('oxid')>-1 or c2.find('energ')>-1 or c2.find('mitoc')>-1 or c2.find('Oxid')>-1 or c2.find('Energ')>-1 or c2.find('Mitoc')>-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "Filtering with c9.find('polar')>-1, \r\nkept 50.00% of 10 valid lines (10 total lines).\r\n", "peek": "polar_ABC+GRZ\tBile secretion\t18\t265298562743.0\t0.435046133126\t89.0\t0.009706903976\tENSCAFT00000003704.ENSCAFT00000003971.ENSCAFT00000004976.ENSCAFT00000006552.ENSCAFT00000007465.ENSCAFT00000008769.ENSCAFT00000011373.ENSCAFT00000015149.ENSCAFT00000015776.ENS\nCAFT00000019177.ENSCAFT00000019466.ENSCAFT00000019757.ENSCAFT00000020561.ENSCAFT00000021332.ENSCAFT00000027259.ENSCAFT00000027704.ENSCAFT00000029367.ENSCAFT00000037977\tpolar\n\npolar_ABC+GRZ\tCell cycle\t19\t132919410090.0\t0.759699050046\t90.5\t0.00379852992534\tENSCAFT00000001725.ENSCAFT00000001862.ENSCAFT00000003425.ENSCAFT00000003463.ENSCAFT00000004945.ENSCAFT00000005562.ENSCAFT00000010616.ENSCAFT00000010664.ENSCAFT00000011883.ENSCA\nFT00000014969.ENSCAFT00000016879.ENSCAFT00000018932.ENSCAFT00000021002.ENSCAFT00000023166.ENSCAFT00000025560.ENSCAFT00000026465.ENSCAFT00000030508.ENSCAFT00000030570.ENSCAFT00000030976\tpolar\n\npolar_ABC+GRZ\tHepatitis C\t16\t123721615870.0\t0.645352706277\t75.5\t0.022045853716\tENSCAFT00000000897.ENSCAFT00000006305.ENSCAFT00000010257.ENSCAFT00000014017.ENSCAFT00000014032.ENSCAFT00000014194.ENSCAFT00000014202.ENSCAFT00000015231.ENSCAFT00000017863.ENSCAF\nT00000024017.ENSCAFT00000026465.ENSCAFT00000027550.ENSCAFT00000027678.ENSCAFT00000029177.ENSCAFT00000031062.ENSCAFT00000039509\tpolar\n", "update_time": "2013-06-18 17:03:12.145233", "name": "(Method 3B) Pathways with average KaKs polar > ABC-GRZ (UMannW statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25184.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-18 17:02:38.618558", "hid": 123, "annotation": "None", "blurb": "5 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 5, "column_types": ["str", "str", "int", "float", "float", "float", "float", "str", "str"], "columns": 9}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [124], "output_datasets": [126], "state": "ok", "params": {"cond": "c2.find('ATP')>-1 or c2.find('oxid')>-1 or c2.find('energ')>-1 or c2.find('mitoc')>-1 or c2.find('Oxid')>-1 or c2.find('Energ')>-1 or c2.find('Mitoc')>-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "Filtering with c9.find('ABC-GRZ')>-1, \r\nkept 50.00% of 10 valid lines (10 total lines).\r\n", "peek": "polar_ABC+GRZ\tArrhythmogenic right ventricular cardiomyopathy (ARVC)\t22\t0.252258414351\t192576679701.0\t99.5\t0.000331244771989\tENSCAFT00000000090.ENSCAFT00000004270.ENSCAFT00000006184.ENSCAFT00000009445.ENSCAFT00000011472.ENSCAFT00000012528.ENSCAFT0000001412\n6.ENSCAFT00000015962.ENSCAFT00000016656.ENSCAFT00000017321.ENSCAFT00000017810.ENSCAFT00000018075.ENSCAFT00000021853.ENSCAFT00000022461.ENSCAFT00000023277.ENSCAFT00000025343.ENSCAFT00000027712.ENSCAFT00000027856.ENSCAFT00000029260.ENSCAFT00000029284.ENSCAFT\n00000036842.ENSCAFT00000037064\tABC-GRZ\n\npolar_ABC+GRZ\tNotch signaling pathway\t10\t0.108455424096\t35327367587.5\t19.0\t0.00892494613439\tENSCAFT00000005426.ENSCAFT00000009074.ENSCAFT00000011198.ENSCAFT00000015366.ENSCAFT00000016879.ENSCAFT00000020970.ENSCAFT00000025527.ENSCAFT00000025565.ENSCAFT00000\n030570.ENSCAFT00000031242\tABC-GRZ\n\npolar_ABC+GRZ\tPhototransduction\t8\t0.375\t405607349145.0\t13.0\t0.020738222107\tENSCAFT00000002572.ENSCAFT00000007461.ENSCAFT00000008452.ENSCAFT00000012650.ENSCAFT00000026758.ENSCAFT00000027651.ENSCAFT00000035729.ENSCAFT00000036012\tABC-GRZ\n", "update_time": "2013-06-18 17:04:07.033560", "name": "(Method 3B) Pathways with average KaKs ABC-GRZ > polar (UMannW statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25185.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-18 17:03:42.318228", "hid": 124, "annotation": "None", "blurb": "5 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 5, "column_types": ["str", "str", "int", "float", "float", "float", "float", "str", "str"], "columns": 9}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [115], "output_datasets": [127], "state": "ok", "params": {"cond": "c9.find('polar')>-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "uploaded tabular file", "peek": "polar_ABC+GRZ\tDNA recombination\t4\t204610578211.0\t0.25\t2.0\t0.0397746675045\tENSCAFT00000001353.ENSCAFT00000007174.ENSCAFT00000009725.ENSCAFT00000010949\tpolar\n\npolar_ABC+GRZ\tGolgi membrane\t15\t61287795712.4\t0.422966268894\t72.0\t0.0431081880079\tENSCAFT00000005661.ENSCAFT00000007546.ENSCAFT00000008956.ENSCAFT00000009848.ENSCAFT00000011305.ENSCAFT00000011885.ENSCAFT00000014931.ENSCAFT00000015692.ENSCAFT00000017086.ENS\nCAFT00000020534.ENSCAFT00000021291.ENSCAFT00000028560.ENSCAFT00000028873.ENSCAFT00000031040.ENSCAFT00000031269\tpolar\n\npolar_ABC+GRZ\tRNA metabolic process\t4\t133262265738.0\t0.0843533018575\t0.0\t0.0102702403156\tENSCAFT00000003862.ENSCAFT00000014352.ENSCAFT00000024618.ENSCAFT00000030290\tpolar\n\npolar_ABC+GRZ\tT cell differentiation in thymus\t10\t81844231284.2\t0.743428195087\t23.5\t0.0208675336957\tENSCAFT00000005426.ENSCAFT00000005687.ENSCAFT00000008272.ENSCAFT00000009725.ENSCAFT00000010616.ENSCAFT00000010949.ENSCAFT00000023308.ENSCAFT00000026465.ENSC\nAFT00000030498.ENSCAFT00000030997\tpolar\n", "update_time": "2013-06-18 16:44:56.791409", "name": "(Method 3B) GO terms with average KaKs polar and ABC-GRZ (UMannW statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25176.dat", "tags": {}, "deleted": false, "designation": null, "parent_id": null, "create_time": "2013-06-18 16:44:40.190950", "hid": 115, "annotation": "None", "blurb": "114 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 114, "column_types": ["str", "str", "int", "float", "float", "float", "float", "str", "str"], "columns": 9}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [115], "output_datasets": [128], "state": "ok", "params": {"cond": "c9.find('ABC-GRZ')>-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "uploaded tabular file", "peek": "polar_ABC+GRZ\tDNA recombination\t4\t204610578211.0\t0.25\t2.0\t0.0397746675045\tENSCAFT00000001353.ENSCAFT00000007174.ENSCAFT00000009725.ENSCAFT00000010949\tpolar\n\npolar_ABC+GRZ\tGolgi membrane\t15\t61287795712.4\t0.422966268894\t72.0\t0.0431081880079\tENSCAFT00000005661.ENSCAFT00000007546.ENSCAFT00000008956.ENSCAFT00000009848.ENSCAFT00000011305.ENSCAFT00000011885.ENSCAFT00000014931.ENSCAFT00000015692.ENSCAFT00000017086.ENS\nCAFT00000020534.ENSCAFT00000021291.ENSCAFT00000028560.ENSCAFT00000028873.ENSCAFT00000031040.ENSCAFT00000031269\tpolar\n\npolar_ABC+GRZ\tRNA metabolic process\t4\t133262265738.0\t0.0843533018575\t0.0\t0.0102702403156\tENSCAFT00000003862.ENSCAFT00000014352.ENSCAFT00000024618.ENSCAFT00000030290\tpolar\n\npolar_ABC+GRZ\tT cell differentiation in thymus\t10\t81844231284.2\t0.743428195087\t23.5\t0.0208675336957\tENSCAFT00000005426.ENSCAFT00000005687.ENSCAFT00000008272.ENSCAFT00000009725.ENSCAFT00000010616.ENSCAFT00000010949.ENSCAFT00000023308.ENSCAFT00000026465.ENSC\nAFT00000030498.ENSCAFT00000030997\tpolar\n", "update_time": "2013-06-18 16:44:56.791409", "name": "(Method 3B) GO terms with average KaKs polar and ABC-GRZ (UMannW statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25176.dat", "tags": {}, "deleted": false, "designation": null, "parent_id": null, "create_time": "2013-06-18 16:44:40.190950", "hid": 115, "annotation": "None", "blurb": "114 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 114, "column_types": ["str", "str", "int", "float", "float", "float", "float", "str", "str"], "columns": 9}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [127], "output_datasets": [129], "state": "ok", "params": {"cond": "c2.find('ATP')>-1 or c2.find('oxid')>-1 or c2.find('energ')>-1 or c2.find('mitoc')>-1 or c2.find('Oxid')>-1 or c2.find('Energ')>-1 or c2.find('Mitoc')>-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "Filtering with c9.find('polar')>-1, \r\nkept 38.60% of 114 valid lines (114 total lines).\r\n", "peek": "polar_ABC+GRZ\tDNA recombination\t4\t204610578211.0\t0.25\t2.0\t0.0397746675045\tENSCAFT00000001353.ENSCAFT00000007174.ENSCAFT00000009725.ENSCAFT00000010949\tpolar\n\npolar_ABC+GRZ\tGolgi membrane\t15\t61287795712.4\t0.422966268894\t72.0\t0.0431081880079\tENSCAFT00000005661.ENSCAFT00000007546.ENSCAFT00000008956.ENSCAFT00000009848.ENSCAFT00000011305.ENSCAFT00000011885.ENSCAFT00000014931.ENSCAFT00000015692.ENSCAFT00000017086.ENS\nCAFT00000020534.ENSCAFT00000021291.ENSCAFT00000028560.ENSCAFT00000028873.ENSCAFT00000031040.ENSCAFT00000031269\tpolar\n\npolar_ABC+GRZ\tRNA metabolic process\t4\t133262265738.0\t0.0843533018575\t0.0\t0.0102702403156\tENSCAFT00000003862.ENSCAFT00000014352.ENSCAFT00000024618.ENSCAFT00000030290\tpolar\n\npolar_ABC+GRZ\tT cell differentiation in thymus\t10\t81844231284.2\t0.743428195087\t23.5\t0.0208675336957\tENSCAFT00000005426.ENSCAFT00000005687.ENSCAFT00000008272.ENSCAFT00000009725.ENSCAFT00000010616.ENSCAFT00000010949.ENSCAFT00000023308.ENSCAFT00000026465.ENSC\nAFT00000030498.ENSCAFT00000030997\tpolar\n", "update_time": "2013-06-18 17:13:48.310778", "name": "(Method 3B) GO terms with average KaKs polar > ABC-GRZ (UMannW statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25188.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-18 17:12:58.714109", "hid": 127, "annotation": "None", "blurb": "44 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 44, "column_types": ["str", "str", "int", "float", "float", "float", "float", "str", "str"], "columns": 9}}}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [128], "output_datasets": [130], "state": "ok", "params": {"cond": "c2.find('ATP')>-1 or c2.find('oxid')>-1 or c2.find('energ')>-1 or c2.find('mitoc')>-1 or c2.find('Oxid')>-1 or c2.find('Energ')>-1 or c2.find('Mitoc')>-1", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "Filtering with c9.find('ABC-GRZ')>-1, \r\nkept 61.40% of 114 valid lines (114 total lines).\r\n", "peek": "polar_ABC+GRZ\tC2H2 zinc finger domain binding\t4\t0.5\t517373470402.0\t2.0\t0.0369029492877\tENSCAFT00000004031.ENSCAFT00000006644.ENSCAFT00000011914.ENSCAFT00000017891\tABC-GRZ\n\npolar_ABC+GRZ\tRac guanyl-nucleotide exchange factor activity\t6\t0.166666666667\t43850994771.8\t7.0\t0.0364365771562\tENSCAFT00000006766.ENSCAFT00000011396.ENSCAFT00000012231.ENSCAFT00000019642.ENSCAFT00000026895.ENSCAFT00000029523\tABC-GRZ\n\npolar_ABC+GRZ\tacetyltransferase activity\t5\t8.11699688622e-13\t45742167009.2\t2.0\t0.0136613341731\tENSCAFT00000008642.ENSCAFT00000009358.ENSCAFT00000024383.ENSCAFT00000026659.ENSCAFT00000030570\tABC-GRZ\n\npolar_ABC+GRZ\talpha-actinin binding\t3\t0.139380507967\t515484061932.0\t0.0\t0.0247673068842\tENSCAFT00000014756.ENSCAFT00000015327.ENSCAFT00000017810\tABC-GRZ\n\npolar_ABC+GRZ\tanagen\t3\t4.58304956391e-13\t787712349210.0\t0.0\t0.0247673068842\tENSCAFT00000029177.ENSCAFT00000031242.ENSCAFT00000035558\tABC-GRZ\n\npolar_ABC+GRZ\tanatomical structure morphogenesis\t4\t0.25\t35233598864.5\t1.5\t0.0263849392379\tENSCAFT00000001265.ENSCAFT00000023312.ENSCAFT00000026658.ENSCAFT00000028054\tABC-GRZ\n", "update_time": "2013-06-18 17:17:16.495743", "name": "(Method 3B) GO terms with average KaKs ABC-GRZ > polar  (UMannW statistically significant)", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25189.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-18 17:16:50.853843", "hid": 128, "annotation": "None", "blurb": "70 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 70, "column_types": ["str", "str", "int", "float", "float", "float", "float", "str", "str"], "columns": 9}}}}, {"tool_id": "toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_new_oscar/1.0.0", "tool_version": "1.0.0", "input_datasets": [66], "output_datasets": [69], "state": "ok", "params": {"ensembl_col": "3", "input": {"info": "Filtering with c14.find('damaging')>-1, \r\nkept 7.58% of 7635 valid lines (7635 total lines).\r\n", "peek": "chr1\t101020385\tENSCAFT00000003500\tENSCAFP00000003246\tC\t523\tR\t86.7\t1079\t476357\t101020385chr1\t476357\tN\tdamaging\n\nchr1\t102877196\tENSCAFT00000003748\tENSCAFP00000003466\tT\t210\tA\t90.3\t83\tU\t102877196chr1\tU\tN\tdamaging\n\nchr30\t10462254\tENSCAFT00000014399\tENSCAFP00000013316\tQ\t1156\tE\t88.1\t184\t100856190\t10462254chr30\t487491\tcfa00562=Inositol phosphate metabolism.cfa01100=Metabolic pathways.cfa04020=Calcium signaling pathway.cfa04062=Chemokine signaling pathway.cfa04070=Phosph\natidylinositol signaling system.cfa04270=Vascular smooth muscle contraction.cfa04310=Wnt signaling pathway.cfa04540=Gap junction.cfa04720=Long-term potentiation.cfa04724=Glutamatergic synapse.cfa04725=Cholinergic synapse.cfa04728=Dopaminergic synapse.cfa04\n730=Long-term depression.cfa04912=GnRH signaling pathway.cfa04916=Melanogenesis.cfa04961=Endocrine and other factor-regulated calcium reabsorption.cfa04970=Salivary secretion.cfa04971=Gastric acid secretion.cfa04972=Pancreatic secretion.cfa05010=Alzheimer'\ns disease.cfa05016=Huntington's disease.cfa05142=Chagas disease (American trypanosomiasis).cfa05143=African trypanosomiasis.cfa05146=Amoebiasis\tdamaging\n", "update_time": "2013-06-17 05:21:54.324021", "name": "(Method 2) Polyphen Damaging prediction on Genes with fixed different alleles in Polar and ABC-GRZ bears", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25001.dat", "tags": {}, "deleted": false, "designation": "out_file1", "parent_id": null, "create_time": "2013-06-17 05:21:25.082350", "hid": 66, "annotation": "None", "blurb": "579 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 579, "column_types": ["str", "int", "str", "str", "str", "int", "str", "float", "int", "str", "str", "str", "str", "str"], "columns": 14}}, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2"}}, {"tool_id": "toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_calc_freq/1.1.0", "tool_version": "1.1.0", "input_datasets": [69], "output_datasets": [70], "state": "ok", "params": {"kgene": "15", "output_format": "a", "kpath": "16", "dbkey": "canFam2", "input": {"info": "", "peek": 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secretion.cfa04972=Pancreatic secretion.cfa05010=Alzheimer'\ns disease.cfa05016=Huntington's disease.cfa05142=Chagas disease (American trypanosomiasis).cfa05143=African trypanosomiasis.cfa05146=Amoebiasis\tdamaging\t487491\tcfa00562=Inositol phosphate metabolism.cfa01100=Metabolic pathways.cfa04020=Calcium signaling pa", "update_time": "2013-06-17 05:26:48.455172", "name": "(Method 2) Get Pathways on Polyphen Damaging prediction on Genes with fixed different alleles in Polar and ABC-GRZ bears", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25004.dat", "tags": {}, "deleted": false, "designation": "output", "parent_id": null, "create_time": "2013-06-17 05:26:25.307145", "hid": 69, "annotation": "None", "blurb": "579 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 579, "column_types": ["str", "int", "str", "str", "str", "int", "str", "float", "int", "str", "str", "str", "str", "str", "str", "str"], "columns": 16}}, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len"}}, {"tool_id": "Filter1", "tool_version": "1.1.0", "input_datasets": [70], "output_datasets": [71], "state": "ok", "params": {"cond": "c4<=0.05", "header_lines": 0, "chromInfo": "/scratch/galaxy/home/tadpole/galaxy_tadpole/tool-data/shared/ucsc/chrom/canFam2.len", "dbkey": "canFam2", "input": {"info": "", "peek": "2\t0.15\t1\t0.022\tcfa00900=Terpenoid backbone biosynthesis\n\n1\t0.12\t2\t0.13\tcfa00072=Synthesis and degradation of ketone bodies\n\n1\t0.11\t3\t0.15\tcfa00062=Fatty acid elongation\n\n6\t0.091\t4\t0.0012\tcfa04920=Adipocytokine signaling pathway\n\n5\t0.091\t4\t0.0031\tcfa00562=Inositol phosphate metabolism\n\n1\t0.091\t4\t0.18\tcfa00790=Folate biosynthesis\n", "update_time": "2013-06-17 05:28:05.203276", "name": "(Method 2) Rank Pathways on Polyphen Damaging prediction on Genes with fixed different alleles in Polar and ABC-GRZ bears", "extension": "tabular", "visible": true, "__HistoryDatasetAssociation__": true, "file_name": "/scratch/galaxy/home/tadpole/galaxy_tadpole/database/files/025/dataset_25005.dat", "tags": {}, "deleted": false, "designation": "output", "parent_id": null, "create_time": "2013-06-17 05:27:34.147914", "hid": 70, "annotation": "None", "blurb": "241 lines", "metadata": {"column_names": null, "comment_lines": null, "dbkey": "canFam2", "data_lines": 241, "column_types": ["int", "float", "int", "float", "str"], "columns": 5}}}}, {"tool_id": "mergeCols1", "tool_version": "1.0.1", "input_datasets": [66], "output_datasets": [72], "state": "ok", "params": {"input1": {"info": "Filtering with c14.find('damaging')>-1, \r\nkept 7.58% of 7635 valid lines (7635 total lines).\r\n", "peek": 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