Mercurial > repos > drosofff > metavisitor_workflows

annotate Galaxy-Workflow-Metavisitor__Workflow_for_small_RNA_profiling_of_contigs.ga @ 3:ba15c770fd40 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
author drosofff
date Thu, 17 Nov 2016 07:27:04 -0500
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ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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1 {
ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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2 "a_galaxy_workflow": "true",
ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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3 "annotation": "",
ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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4 "format-version": "0.1",
ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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5 "name": "Metavisitor: Workflow for small RNA profiling of contigs",
ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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6 "steps": {
ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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7 "0": {
ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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8 "annotation": "",
ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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13 {
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15 "name": "Input Dataset Collection of fastq reads"
ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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16 }
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19 "name": "Input dataset collection",
ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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20 "outputs": [],
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29 "type": "data_collection_input",
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31 "workflow_outputs": [
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47 "name": "de novo assembled Oases contigs"
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61 "type": "data_input",
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63 "workflow_outputs": [
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89 "outputs": [
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107 },
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147 {
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159 "newname": "Contig (>300 nt)"
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161 "action_type": "RenameDatasetAction",
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162 "output_name": "output"
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164 },
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165 "tool_errors": null,
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167 "tool_shed_repository": {
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168 "changeset_revision": "c8cd0a03db49",
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169 "name": "fasta_filter_by_length",
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170 "owner": "devteam",
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171 "tool_shed": "toolshed.g2.bx.psu.edu"
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173 "tool_state": "{\"__page__\": 0, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"300\\\"\"}",
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174 "tool_version": "1.1",
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175 "type": "tool",
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185 "4": {
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186 "annotation": "",
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187 "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2",
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221 },
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227 "owner": "mvdbeek",
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229 },
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231 "tool_version": "0.2",
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235 {
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237 "output_name": "out_file1",
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241 },
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244 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0",
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246 "input_connections": {
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247 "input": {
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248 "id": 3,
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249 "output_name": "output"
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250 }
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251 },
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252 "inputs": [
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253 {
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254 "description": "runtime parameter for tool Regex Find And Replace",
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255 "name": "input"
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256 }
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257 ],
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258 "label": null,
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259 "name": "Regex Find And Replace",
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260 "outputs": [
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261 {
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262 "name": "out_file1",
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263 "type": "input"
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264 }
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266 "position": {
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269 },
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270 "post_job_actions": {
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271 "RenameDatasetActionout_file1": {
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272 "action_arguments": {
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273 "newname": "contig (>300t, simplified names)"
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274 },
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275 "action_type": "RenameDatasetAction",
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276 "output_name": "out_file1"
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278 },
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279 "tool_errors": null,
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280 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0",
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281 "tool_shed_repository": {
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282 "changeset_revision": "9ea374bb0350",
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283 "name": "regex_find_replace",
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284 "owner": "jjohnson",
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348 },
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349 "HideDatasetActionunaligned": {
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352 "output_name": "unaligned"
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354 },
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355 "tool_errors": null,
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356 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1",
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357 "tool_shed_repository": {
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358 "changeset_revision": "615d2550977f",
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359 "name": "msp_sr_bowtie",
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360 "owner": "drosofff",
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361 "tool_shed": "toolshed.g2.bx.psu.edu"
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362 },
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364 "tool_version": "1.1.2.1",
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365 "type": "tool",
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368 {
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375 "7": {
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380 "refGenomeSource|ownFile": {
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383 },
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430 "action_type": "HideDatasetAction",
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431 "output_name": "readmap_dataframe"
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432 },
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434 "action_arguments": {},
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436 "output_name": "size_distribution_dataframe"
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438 },
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439 "tool_errors": null,
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440 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.2.0",
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441 "tool_shed_repository": {
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442 "changeset_revision": "92898cc3ea19",
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443 "name": "msp_sr_readmap_and_size_histograms",
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444 "owner": "drosofff",
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445 "tool_shed": "toolshed.g2.bx.psu.edu"
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446 },
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448 "tool_version": "1.2.0",
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449 "type": "tool",
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450 "uuid": "87f9f9b5-5c71-465b-9422-c0696a3048a5",
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451 "workflow_outputs": [
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452 {
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453 "label": null,
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454 "output_name": "size_PDF",
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455 "uuid": "91fa9c78-72dd-41e8-9937-c4b44682f79b"
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456 },
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459 "output_name": "combi_PDF",
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461 },
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464 "output_name": "readmap_PDF",
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469 },
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470 "uuid": "c3853e65-8d66-47fc-aad9-6a40f5517622"
ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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471 }