Mercurial > repos > peterjc > secreted_protein_workflow

annotate secreted_protein_workflow.ga @ 4:b14c822a37fe draft

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Uploaded v0.0.1d, README file with clearer citation instructions.
author peterjc
date Mon, 19 Aug 2013 11:38:03 -0400
parents 3a6de5cb858d
children 36b2c2b5051e
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "Runs SignalP v3.0 and TMHMM v2.0 to look for secreted proteins.",
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4 "format-version": "0.1",
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5 "name": "Find secreted proteins with TMHMM and SignalP",
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175 }
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176 ],
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190 "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
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195 "5": {
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196 "annotation": "Select proteins with no predicted transmembrane helices.",
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202 }
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203 },
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205 "name": "Filter",
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207 {
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208 "name": "out_file1",
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209 "type": "input"
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210 }
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211 ],
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215 },
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219 "action_type": "HideDatasetAction",
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220 "output_name": "out_file1"
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221 },
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222 "RenameDatasetActionout_file1": {
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223 "action_arguments": {
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224 "newname": "Filtered TMHMM results"
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225 },
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226 "action_type": "RenameDatasetAction",
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227 "output_name": "out_file1"
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228 }
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229 },
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230 "tool_errors": null,
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231 "tool_id": "Filter1",
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232 "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c5== 0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}",
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233 "tool_version": "1.1.0",
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234 "type": "tool",
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236 },
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237 "6": {
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238 "annotation": "Select those sequences with no transmembrane helices (from those with signal peptides).",
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239 "id": 6,
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240 "input_connections": {
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243 "output_name": "output_pos"
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244 },
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247 "output_name": "out_file1"
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248 }
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249 },
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250 "inputs": [],
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251 "name": "Filter sequences by ID",
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252 "outputs": [
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253 {
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254 "name": "output_pos",
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255 "type": "fasta"
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256 },
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257 {
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259 "type": "fasta"
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260 }
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261 ],
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265 },
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269 "action_type": "HideDatasetAction",
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271 },
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273 "action_arguments": {
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274 "newname": "Secreted proteins"
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275 },
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276 "action_type": "RenameDatasetAction",
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277 "output_name": "output_pos"
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278 }
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279 },
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280 "tool_errors": null,
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282 "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}",
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283 "tool_version": "0.0.1",
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284 "type": "tool",
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285 "user_outputs": []
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286 }
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287 }
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288 }