annotate GeneSeqToFamily.ga @ 6:266800d51605 draft

"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
author earlhaminst
date Thu, 10 Jun 2021 16:18:59 +0000
parents cc5419f7dff7
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266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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180 },
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181 "HideDatasetActionoutput": {
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diff changeset
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266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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183 "action_type": "HideDatasetAction",
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diff changeset
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266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
185 }
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
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diff changeset
186 },
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
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266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
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diff changeset
190 "name": "filter_by_fasta_ids",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
191 "owner": "galaxyp",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
192 "tool_shed": "toolshed.g2.bx.psu.edu"
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
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diff changeset
193 },
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
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diff changeset
194 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"dedup\": \"\\\"true\\\"\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"header_criteria\": \"{\\\"__current_case__\\\": 0, \\\"header_criteria_select\\\": \\\"\\\"}\", \"output_discarded\": \"\\\"true\\\"\", \"sequence_criteria\": \"{\\\"__current_case__\\\": 2, \\\"regexp\\\": \\\"^[^*]+$\\\", \\\"sequence_criteria_select\\\": \\\"regexp\\\"}\"}",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
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diff changeset
195 "tool_version": "2.2",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
196 "type": "tool",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
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diff changeset
198 "workflow_outputs": []
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
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diff changeset
199 },
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
201 "annotation": "",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
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diff changeset
204 "id": 5,
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
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diff changeset
206 "input": {
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diff changeset
207 "id": 4,
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
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diff changeset
208 "output_name": "output"
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
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diff changeset
209 }
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
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diff changeset
210 },
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
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diff changeset
211 "inputs": [
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
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diff changeset
212 {
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
213 "description": "runtime parameter for tool faSplit",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
214 "name": "O"
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
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diff changeset
215 }
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
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diff changeset
216 ],
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
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266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
218 "name": "faSplit",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
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diff changeset
219 "outputs": [
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earlhaminst
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diff changeset
220 {
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diff changeset
221 "name": "output_list",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
222 "type": "input"
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
223 }
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
224 ],
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diff changeset
225 "position": {
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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226 "left": 845.96875,
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diff changeset
228 },
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
229 "post_job_actions": {
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
230 "HideDatasetActionoutput_list": {
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
231 "action_arguments": {},
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
232 "action_type": "HideDatasetAction",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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233 "output_name": "output_list"
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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234 }
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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235 },
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
236 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fasplit/fasplit/332",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
237 "tool_shed_repository": {
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diff changeset
238 "changeset_revision": "dc36d50254d8",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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diff changeset
239 "name": "ucsc_fasplit",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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240 "owner": "iuc",
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241 "tool_shed": "toolshed.g2.bx.psu.edu"
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242 },
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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243 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"O\": \"{\\\"__current_case__\\\": 0, \\\"count\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"split_type\\\": \\\"sequence\\\"}\", \"__page__\": null}",
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244 "tool_version": "332",
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245 "type": "tool",
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247 "workflow_outputs": []
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248 },
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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255 "input_file": {
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256 "id": 4,
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257 "output_name": "output"
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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258 }
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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259 },
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261 {
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264 }
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265 ],
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269 {
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270 "name": "outfile",
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271 "type": "data"
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272 }
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277 },
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280 "action_arguments": {},
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281 "action_type": "HideDatasetAction",
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282 "output_name": "outfile"
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283 }
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284 },
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286 "tool_shed_repository": {
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288 "name": "ncbi_blast_plus",
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289 "owner": "devteam",
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290 "tool_shed": "toolshed.g2.bx.psu.edu"
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291 },
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292 "tool_state": "{\"__page__\": null, \"mask_data_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"dbtype\": \"\\\"prot\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"true\\\"\", \"tax\": \"{\\\"__current_case__\\\": 0, \\\"taxselect\\\": \\\"\\\"}\", \"title\": \"\\\"\\\"\", \"parse_seqids\": \"\\\"false\\\"\"}",
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293 "tool_version": "0.3.0",
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294 "type": "tool",
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295 "uuid": "c72477fb-cc1d-45ec-a0cd-8215be8fe8ee",
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296 "workflow_outputs": []
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297 },
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298 "7": {
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299 "annotation": "",
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266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
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300 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.0",
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301 "errors": null,
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302 "id": 7,
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303 "input_connections": {
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304 "db_opts|histdb": {
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305 "id": 6,
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306 "output_name": "outfile"
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307 },
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308 "query": {
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309 "id": 5,
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310 "output_name": "output_list"
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311 }
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312 },
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313 "inputs": [],
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314 "label": null,
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315 "name": "NCBI BLAST+ blastp",
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316 "outputs": [
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317 {
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416 "tool_shed_repository": {
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418 "name": "blast_parser",
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419 "owner": "earlhaminst",
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424 "type": "tool",
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426 "workflow_outputs": [
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427 {
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428 "label": null,
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429 "output_name": "output",
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431 }
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432 ]
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433 },
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438 "id": 10,
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439 "input_connections": {
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440 "inputFile": {
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441 "id": 9,
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442 "output_name": "output"
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443 }
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444 },
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445 "inputs": [
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446 {
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447 "description": "runtime parameter for tool hcluster_sg",
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448 "name": "c_conditional"
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452 "name": "hcluster_sg",
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453 "outputs": [
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454 {
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455 "name": "outputFile",
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456 "type": "tabular"
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459 "position": {
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460 "left": 1544.875,
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462 },
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463 "post_job_actions": {},
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464 "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg/hcluster_sg/0.5.1.1",
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465 "tool_shed_repository": {
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467 "name": "hcluster_sg",
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468 "owner": "earlhaminst",
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469 "tool_shed": "toolshed.g2.bx.psu.edu"
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470 },
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471 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"c_conditional\": \"{\\\"C\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"L\\\": \\\"2\\\", \\\"O\\\": {\\\"O_selector\\\": \\\"\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"b\\\": \\\"0.1\\\", \\\"c\\\": \\\"\\\", \\\"m\\\": \\\"500\\\", \\\"s\\\": \\\"0.34\\\"}\", \"w\": \"\\\"0\\\"\", \"inputFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
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diff changeset
944 "label": null,
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
parents: 4
diff changeset
945 "output_name": "homology",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
parents: 4
diff changeset
946 "uuid": "d20dba82-b0c5-41d7-9f2e-f67240548967"
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
parents: 4
diff changeset
947 }
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
parents: 4
diff changeset
948 ]
0
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
949 }
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
950 },
4
cc5419f7dff7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit efb6a192c36d4e8aa6d24d692890025ffd8a0e65-dirty
earlhaminst
parents: 2
diff changeset
951 "tags": [],
6
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
parents: 4
diff changeset
952 "uuid": "45eedb69-98b5-4ea2-9f17-791fa54ef823",
266800d51605 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
earlhaminst
parents: 4
diff changeset
953 "version": 20
4
cc5419f7dff7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit efb6a192c36d4e8aa6d24d692890025ffd8a0e65-dirty
earlhaminst
parents: 2
diff changeset
954 }