annotate Galaxy-Workflow-ABRF_2017_Workflow_for_Functional_Comparison.ga @ 1:338a6d724774 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777
author galaxyp
date Thu, 16 Mar 2017 08:45:23 -0400
parents eb71034189fb
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eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
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175 },
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176 "tables_1|table": {
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177 "id": 1,
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178 "output_name": "output"
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179 },
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180 "tables_2|table": {
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181 "id": 2,
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182 "output_name": "output"
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183 },
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184 "tables_3|table": {
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185 "id": 3,
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186 "output_name": "output"
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187 },
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188 "tables_4|table": {
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189 "id": 4,
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190 "output_name": "output"
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191 }
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192 },
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193 "inputs": [
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194 {
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195 "description": "runtime parameter for tool Query Tabular",
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196 "name": "add_to_database"
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197 }
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198 ],
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199 "label": null,
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200 "name": "Query Tabular",
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201 "outputs": [
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202 {
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galaxyp
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203 "name": "sqlitedb",
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204 "type": "sqlite"
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205 },
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206 {
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207 "name": "output",
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208 "type": "tabular"
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209 }
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210 ],
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211 "position": {
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212 "left": 440,
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213 "top": 230
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214 },
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galaxyp
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215 "post_job_actions": {
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216 "RenameDatasetActionoutput": {
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217 "action_arguments": {
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218 "newname": "BIOLOGICAL PROCESS COMPARISON"
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219 },
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220 "action_type": "RenameDatasetAction",
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221 "output_name": "output"
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222 }
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223 },
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224 "tool_errors": null,
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225 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0",
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226 "tool_shed_repository": {
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227 "changeset_revision": "ae27dab228b8",
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228 "name": "query_tabular",
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229 "owner": "jjohnson",
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230 "tool_shed": "toolshed.g2.bx.psu.edu"
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231 },
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232 "tool_state": "{\"tables\": \"[{\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"false\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"go\\\", \\\"col_names\\\": \\\"aspect,go_id,description\\\", \\\"indexes\\\": [{\\\"__index__\\\": 0, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"go_id\\\"}, {\\\"__index__\\\": 1, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"aspect,go_id,description\\\"}]}, \\\"__index__\\\": 0, \\\"input_opts\\\": {\\\"linefilters\\\": []}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"false\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"bering\\\", \\\"col_names\\\": \\\"peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_reference,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids\\\", \\\"indexes\\\": [{\\\"__index__\\\": 0, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"go_reference,peptide\\\"}]}, \\\"__index__\\\": 1, \\\"input_opts\\\": {\\\"linefilters\\\": [{\\\"filter\\\": {\\\"comment_char\\\": \\\"#\\\", \\\"__current_case__\\\": 1, \\\"filter_type\\\": \\\"comment\\\"}, \\\"__index__\\\": 0}]}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"false\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"chukchi\\\", \\\"col_names\\\": \\\"peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_reference,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids\\\", \\\"indexes\\\": [{\\\"__index__\\\": 0, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"go_reference,peptide\\\"}]}, \\\"__index__\\\": 2, \\\"input_opts\\\": {\\\"linefilters\\\": [{\\\"filter\\\": {\\\"comment_char\\\": \\\"#\\\", \\\"__current_case__\\\": 1, \\\"filter_type\\\": \\\"comment\\\"}, \\\"__index__\\\": 0}]}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"true\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"bering_psms\\\", \\\"col_names\\\": \\\"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\", \\\"indexes\\\": []}, \\\"__index__\\\": 3, \\\"input_opts\\\": {\\\"linefilters\\\": [{\\\"filter\\\": {\\\"regex_action\\\": \\\"include_match\\\", \\\"regex_pattern\\\": \\\"^\\\\\\\\d\\\", \\\"__current_case__\\\": 2, \\\"filter_type\\\": \\\"regex\\\"}, \\\"__index__\\\": 0}]}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"true\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"chukchi_psms\\\", \\\"col_names\\\": \\\"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\", \\\"indexes\\\": []}, \\\"__index__\\\": 4, \\\"input_opts\\\": {\\\"linefilters\\\": [{\\\"filter\\\": {\\\"regex_action\\\": \\\"include_match\\\", \\\"regex_pattern\\\": \\\"^\\\\\\\\d\\\", \\\"__current_case__\\\": 2, \\\"filter_type\\\": \\\"regex\\\"}, \\\"__index__\\\": 0}]}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\", \"save_db\": \"\\\"true\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\", \"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\",count(distinct c.peptide) as \\\\\\\"chukchi_peptides\\\\\\\",\\\\ncount(distinct b.id)*1.42 as \\\\\\\"bering_psms\\\\\\\", count(distinct c.id) as \\\\\\\"chukchi_psms\\\\\\\"\\\\n FROM go as g LEFT OUTER JOIN\\\\n ( SELECT go.description, bering.peptide, bering_psms.id\\\\n FROM go LEFT OUTER JOIN bering ON go.go_id = bering.go_reference JOIN bering_psms ON bering.peptide = bering_psms.sequence\\\\n GROUP BY go.description, bering.peptide, bering_psms.id\\\\n ) as b ON g.description = b.description LEFT OUTER JOIN\\\\n ( SELECT go.description, chukchi.peptide, chukchi_psms.id\\\\n FROM go LEFT OUTER JOIN chukchi ON go.go_id = chukchi.go_reference JOIN chukchi_psms ON chukchi.peptide = chukchi_psms.sequence\\\\n GROUP BY go.description, chukchi.peptide, chukchi_psms.id\\\\n ) as c ON g.description = c.description\\\\nWHERE g.aspect = 'biological_process'\\\\nGROUP BY g.description\\\\nORDER BY abs(bering_peptides - chukchi_peptides) desc, bering_peptides desc,chukchi_peptides desc\\\"\", \"add_to_database\": \"{\\\"withdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"workdb\": \"\\\"workdb.sqlite\\\"\"}",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
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233 "tool_version": "2.0.0",
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234 "type": "tool",
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235 "uuid": "42fb8bde-03c9-4e9d-b003-55d01bb306d6",
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236 "workflow_outputs": [
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237 {
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238 "label": null,
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239 "output_name": "output",
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galaxyp
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240 "uuid": "369c85d5-6d8f-45ca-8f55-01dddce5a4e9"
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241 },
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242 {
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243 "label": null,
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244 "output_name": "sqlitedb",
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galaxyp
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245 "uuid": "fb8dd73d-95c9-48c8-945c-07adf0b13dab"
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246 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
247 ]
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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248 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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249 "6": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
250 "annotation": "",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
251 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
252 "id": 6,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
253 "input_connections": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
254 "sqlitedb": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
255 "id": 5,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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256 "output_name": "sqlitedb"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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257 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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258 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
259 "inputs": [
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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260 {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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261 "description": "runtime parameter for tool SQLite to tabular",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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262 "name": "sqlitedb"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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263 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
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264 ],
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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265 "label": null,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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266 "name": "SQLite to tabular",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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267 "outputs": [
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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268 {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
269 "name": "query_results",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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270 "type": "tabular"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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271 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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272 ],
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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273 "position": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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274 "left": 874,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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275 "top": 204
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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276 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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277 "post_job_actions": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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278 "RenameDatasetActionquery_results": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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279 "action_arguments": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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280 "newname": "MOLECULAR FUNCTION COMPARISON"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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281 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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282 "action_type": "RenameDatasetAction",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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283 "output_name": "query_results"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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284 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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285 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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286 "tool_errors": null,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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287 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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288 "tool_shed_repository": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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289 "changeset_revision": "78e9570fbe08",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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290 "name": "sqlite_to_tabular",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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291 "owner": "jjohnson",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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292 "tool_shed": "toolshed.g2.bx.psu.edu"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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293 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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294 "tool_state": "{\"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\",count(distinct c.peptide) as \\\\\\\"chukchi_peptides\\\\\\\", count(distinct b.id)*1.42 as \\\\\\\"bering_psms\\\\\\\", count(distinct c.id) as \\\\\\\"chukchi_psms\\\\\\\"\\\\nFROM go as g LEFT OUTER JOIN\\\\n ( SELECT go.description, bering.peptide, bering_psms.id\\\\n FROM go LEFT OUTER JOIN bering ON go.go_id = bering.go_reference JOIN bering_psms ON bering.peptide = bering_psms.sequence\\\\n GROUP BY go.description, bering.peptide, bering_psms.id\\\\n ) as b ON g.description = b.description LEFT OUTER JOIN\\\\n ( SELECT go.description, chukchi.peptide, chukchi_psms.id\\\\n FROM go LEFT OUTER JOIN chukchi ON go.go_id = chukchi.go_reference JOIN chukchi_psms ON chukchi.peptide = chukchi_psms.sequence\\\\n GROUP BY go.description, chukchi.peptide, chukchi_psms.id\\\\n ) as c ON g.description = c.description\\\\nWHERE g.aspect = 'molecular_function'\\\\nGROUP BY g.description\\\\nORDER BY abs(bering_peptides - chukchi_peptides) desc, bering_peptides desc,chukchi_peptides desc\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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295 "tool_version": "0.0.1",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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296 "type": "tool",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
297 "uuid": "ee7d5bd3-d2c4-4653-bd55-fa236abfc7f8",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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298 "workflow_outputs": [
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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299 {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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300 "label": null,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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301 "output_name": "query_results",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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302 "uuid": "90cf3457-65be-474d-a43f-ead52ad50e21"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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303 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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304 ]
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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305 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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306 "7": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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307 "annotation": "",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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308 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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309 "id": 7,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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310 "input_connections": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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311 "sqlitedb": {
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galaxyp
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312 "id": 5,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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313 "output_name": "sqlitedb"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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314 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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315 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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316 "inputs": [
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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317 {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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318 "description": "runtime parameter for tool SQLite to tabular",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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319 "name": "sqlitedb"
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galaxyp
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320 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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321 ],
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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322 "label": null,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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323 "name": "SQLite to tabular",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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324 "outputs": [
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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325 {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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326 "name": "query_results",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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327 "type": "tabular"
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galaxyp
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328 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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329 ],
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
330 "position": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
331 "left": 876,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
332 "top": 342
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
333 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
334 "post_job_actions": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
335 "RenameDatasetActionquery_results": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
336 "action_arguments": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
337 "newname": "CELLULAR COMPONENT COMPARISON"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
338 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
339 "action_type": "RenameDatasetAction",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
340 "output_name": "query_results"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
341 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
342 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
343 "tool_errors": null,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
344 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
345 "tool_shed_repository": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
346 "changeset_revision": "78e9570fbe08",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
347 "name": "sqlite_to_tabular",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
348 "owner": "jjohnson",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
349 "tool_shed": "toolshed.g2.bx.psu.edu"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
350 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
351 "tool_state": "{\"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\",count(distinct c.peptide) as \\\\\\\"chukchi_peptides\\\\\\\", count(distinct b.id)*1.42 as \\\\\\\"bering_psms\\\\\\\", count(distinct c.id) as \\\\\\\"chukchi_psms\\\\\\\"\\\\nFROM go as g LEFT OUTER JOIN\\\\n ( SELECT go.description, bering.peptide, bering_psms.id\\\\n FROM go LEFT OUTER JOIN bering ON go.go_id = bering.go_reference JOIN bering_psms ON bering.peptide = bering_psms.sequence\\\\n GROUP BY go.description, bering.peptide, bering_psms.id\\\\n ) as b ON g.description = b.description LEFT OUTER JOIN\\\\n ( SELECT go.description, chukchi.peptide, chukchi_psms.id\\\\n FROM go LEFT OUTER JOIN chukchi ON go.go_id = chukchi.go_reference JOIN chukchi_psms ON chukchi.peptide = chukchi_psms.sequence\\\\n GROUP BY go.description, chukchi.peptide, chukchi_psms.id\\\\n ) as c ON g.description = c.description\\\\nWHERE g.aspect = 'cellular_component'\\\\nGROUP BY g.description\\\\nORDER BY abs(bering_peptides - chukchi_peptides) desc, bering_peptides desc,chukchi_peptides desc\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
352 "tool_version": "0.0.1",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
353 "type": "tool",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
354 "uuid": "d0f27344-2721-47e3-891a-0a9288293945",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
355 "workflow_outputs": [
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
356 {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
357 "label": null,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
358 "output_name": "query_results",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
359 "uuid": "80f8307d-68d7-4a49-bae8-b43957dd3098"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
360 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
361 ]
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
362 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
363 "8": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
364 "annotation": "",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
365 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
366 "id": 8,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
367 "input_connections": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
368 "sqlitedb": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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diff changeset
369 "id": 5,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
370 "output_name": "sqlitedb"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
371 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
372 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
373 "inputs": [
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
374 {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
375 "description": "runtime parameter for tool SQLite to tabular",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
376 "name": "sqlitedb"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
377 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
378 ],
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
379 "label": null,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
380 "name": "SQLite to tabular",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
381 "outputs": [
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
382 {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
383 "name": "query_results",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
384 "type": "tabular"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
385 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
386 ],
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
387 "position": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
388 "left": 883,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
389 "top": 457.5
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
390 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
391 "post_job_actions": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
392 "RenameDatasetActionquery_results": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
393 "action_arguments": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
394 "newname": "PEPTIDE PSM COUNTS COMPARISON"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
395 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
396 "action_type": "RenameDatasetAction",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
397 "output_name": "query_results"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
398 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
399 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
400 "tool_errors": null,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
401 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
402 "tool_shed_repository": {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
403 "changeset_revision": "78e9570fbe08",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
404 "name": "sqlite_to_tabular",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
405 "owner": "jjohnson",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
406 "tool_shed": "toolshed.g2.bx.psu.edu"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
407 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
408 "tool_state": "{\"sqlquery\": \"\\\"SELECT peptides.peptide, count(bering_psms.id)*1.42 as \\\\\\\"BeringStrait_PSMs\\\\\\\", count(chukchi_psms.id) as \\\\\\\"ChukchiSea_PSMs\\\\\\\"\\\\nFROM \\\\n(SELECT distinct sequence \\\\\\\"peptide\\\\\\\" FROM bering_psms UNION SELECT sequence as \\\\\\\"peptide\\\\\\\" FROM chukchi_psms) as peptides\\\\nLEFT JOIN bering_psms ON peptides.peptide = bering_psms.sequence\\\\nLEFT JOIN chukchi_psms ON peptides.peptide = chukchi_psms.sequence\\\\nGROUP BY peptides.peptide\\\\nORDER BY peptides.peptide\\\\n\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
409 "tool_version": "0.0.1",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
parents:
diff changeset
410 "type": "tool",
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411 "uuid": "a3b80420-6655-4acf-b62b-dcb4ac5d9c6e",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
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412 "workflow_outputs": [
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
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413 {
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
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414 "label": null,
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
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415 "output_name": "query_results",
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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416 "uuid": "a9b9c19b-8ab2-4f08-9c1f-73e6991f58f9"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
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417 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
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418 ]
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
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419 }
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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420 },
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
galaxyp
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421 "uuid": "9f54fdad-4b9b-4389-8c3a-4512f0cf8df5"
eb71034189fb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
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422 }