annotate RNA-seq_(SE)_Quantification_-_Mouse.ga @ 2:324f32e70ea4 draft default tip

Update annotations
author stemcellcommons
date Wed, 25 Oct 2017 15:10:22 -0400
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "{\n \"description\": \"Transcript quantification for single-end RNA-seq data. Reads are aligned to the mouse (mm10) reference genome.\",\n \"file_relationship\": {\n \"file_relationship\": {},\n \"value_type\": \"LIST\",\n \"name\": \"List of FASTQ Files\",\n \"input_files\": [\n {\n \"allowed_filetypes\": [{\"name\": \"FASTQ\"}],\n \"name\": \"Input FASTQ\",\n \"description\": \"Input FASTQ File\"\n }\n ]\n }\n}",
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4 "format-version": "0.1",
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5 "name": "RNA-seq (SE) Quantification - Mouse",
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6 "steps": {
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7 "0": {
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13 {
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48 "name": "output_file",
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49 "type": "fastqsanger"
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50 }
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82 "label": null,
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217 "action_arguments": {},
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218 "action_type": "HideDatasetAction",
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219 "output_name": "deletions"
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220 },
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221 "HideDatasetActionfusions": {
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222 "action_arguments": {},
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223 "action_type": "HideDatasetAction",
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224 "output_name": "fusions"
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225 },
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226 "HideDatasetActioninsertions": {
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227 "action_arguments": {},
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228 "action_type": "HideDatasetAction",
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229 "output_name": "insertions"
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230 },
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231 "HideDatasetActionjunctions": {
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232 "action_arguments": {},
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233 "action_type": "HideDatasetAction",
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234 "output_name": "junctions"
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235 },
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236 "HideDatasetActionunmapped": {
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237 "action_arguments": {},
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238 "action_type": "HideDatasetAction",
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239 "output_name": "unmapped"
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240 }
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241 },
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242 "tool_errors": null,
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243 "tool_id": "toolshed.g2.bx.psu.edu/repos/scottx611x/tophat2_with_gene_annotations/tophat2/2.1.0",
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245 "tool_version": "2.1.0",
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246 "type": "tool",
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247 "uuid": "5be0f425-2b8c-498e-8b33-67ffc68382c4",
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248 "workflow_outputs": [
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249 {
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250 "label": null,
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251 "output_name": "accepted_hits",
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252 "uuid": "ac6f0f65-e43d-450e-a495-f76221382d52"
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253 }
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254 ]
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255 },
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256 "4": {
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257 "annotation": "{\n\"output\": {\n\"name\": \"feature_counts\", \"description\": \"\",\n\"type\": \"tabular\"\n},\n\"output_summary\": {\n\"name\": \"feature_counts_summary\", \"description\": \"\",\n\"type\": \"tabular\"\n}\n}",
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258 "content_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5",
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259 "id": 4,
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260 "input_connections": {
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261 "alignments": {
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262 "id": 3,
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263 "output_name": "accepted_hits"
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264 }
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265 },
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266 "inputs": [],
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267 "label": null,
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268 "name": "featureCounts",
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269 "outputs": [
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270 {
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271 "name": "output",
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272 "type": "tabular"
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273 },
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274 {
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275 "name": "output_summary",
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276 "type": "tabular"
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277 }
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278 ],
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279 "position": {
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280 "left": 1458,
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281 "top": 330.5
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282 },
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283 "post_job_actions": {},
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284 "tool_errors": null,
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285 "tool_id": "toolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/featurecounts/1.4.6.p5",
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286 "tool_state": "{\"__page__\": 0, \"reference_gene_sets_source\": \"{\\\"reference_gene_sets\\\": \\\"/mnt/galaxyIndices/gene_annotations/mm10_genes.gtf\\\", \\\"__current_case__\\\": 2, \\\"source_select\\\": \\\"indexed_all\\\"}\", \"format\": \"\\\"tabdel_short\\\"\", \"__rerun_remap_job_id__\": null, \"alignments\": \"null\", \"extended_parameters\": \"{\\\"parameters\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\"}",
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287 "tool_version": "1.4.6.p5",
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288 "type": "tool",
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289 "uuid": "ea7b872b-a80b-4cc4-a3bb-c60839d40560",
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290 "workflow_outputs": [
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291 {
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292 "label": null,
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293 "output_name": "output_summary",
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294 "uuid": "de76250a-8528-44aa-b05d-bf478488598c"
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295 },
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296 {
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297 "label": null,
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298 "output_name": "output",
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299 "uuid": "3674ca27-20db-4ea3-842f-22f34e5b6c65"
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300 }
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301 ]
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302 }
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303 },
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304 "uuid": "cf5014b4-f20e-4c26-bffe-3f32e0079245"
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305 }