annotate Proteomics_Splice_DB_from_Paired_End_RNAseq.ga @ 0:3e7ebf62c90f draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
author galaxyp
date Tue, 10 May 2016 18:12:00 -0400
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "Create a peptide fasta database with novel splice junctions that are inferred from Paired End \nRNAseq data",
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5 "name": "Proteomics Splice DB from Paired End RNAseq",
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6 "steps": {
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7 "0": {
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12 "inputs": [
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15 "name": "RNA-Seq left mate pair fastq"
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16 }
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17 ],
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19 "name": "Input dataset",
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20 "outputs": [],
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24 },
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27 "tool_state": "{\"name\": \"RNA-Seq left mate pair fastq\"}",
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29 "type": "data_input",
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31 "workflow_outputs": [
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47 "name": "RNA-Seq right mate pair fastq"
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48 }
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49 ],
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51 "name": "Input dataset",
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52 "outputs": [],
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56 },
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59 "tool_state": "{\"name\": \"RNA-Seq right mate pair fastq\"}",
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61 "type": "data_input",
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63 "workflow_outputs": [
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66 "output_name": "output",
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72 "annotation": "",
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75 "input_connections": {},
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76 "inputs": [
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93 "type": "data_input",
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96 {
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98 "output_name": "output",
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100 }
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102 },
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103 "3": {
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104 "annotation": "",
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107 "input_connections": {},
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108 "inputs": [
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109 {
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110 "description": "",
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111 "name": "Reference Genome FASTA file"
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112 }
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113 ],
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115 "name": "Input dataset",
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116 "outputs": [],
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120 },
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123 "tool_state": "{\"name\": \"Reference Genome FASTA file\"}",
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125 "type": "data_input",
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126 "uuid": "None",
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127 "workflow_outputs": [
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128 {
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130 "output_name": "output",
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131 "uuid": "c98b5818-3d22-48f9-87bd-48ef64d41aeb"
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132 }
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133 ]
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134 },
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135 "4": {
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136 "annotation": "Allow novel junctions, not from the GTF",
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137 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0",
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138 "id": 4,
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139 "input_connections": {
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140 "input1": {
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141 "id": 0,
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142 "output_name": "output"
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143 },
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144 "refGenomeSource|ownFile": {
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145 "id": 3,
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146 "output_name": "output"
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147 },
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148 "singlePaired|input2": {
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149 "id": 1,
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150 "output_name": "output"
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151 },
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152 "singlePaired|pParams|own_junctions|gene_model_ann|gene_annotation_model": {
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153 "id": 2,
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154 "output_name": "output"
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155 }
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156 },
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157 "inputs": [],
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158 "label": null,
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159 "name": "TopHat for Illumina",
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168 },
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172 },
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176 }
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177 ],
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181 },
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182 "post_job_actions": {},
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183 "tool_errors": null,
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184 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0",
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186 "tool_version": "1.5.0",
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187 "type": "tool",
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188 "uuid": "None",
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189 "workflow_outputs": [
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190 {
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191 "label": null,
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192 "output_name": "deletions",
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194 },
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195 {
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196 "label": null,
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197 "output_name": "insertions",
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199 },
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200 {
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201 "label": null,
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202 "output_name": "accepted_hits",
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203 "uuid": "52a1f08e-c4ae-44c2-b50b-5b49200bad82"
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204 },
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205 {
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206 "label": null,
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207 "output_name": "junctions",
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208 "uuid": "1f95f460-4b20-4ee0-b8d3-bd60c1d29c7e"
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209 }
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210 ]
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211 },
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212 "5": {
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213 "annotation": "Only look for supplied junctions",
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214 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0",
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215 "id": 5,
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216 "input_connections": {
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217 "input1": {
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218 "id": 0,
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219 "output_name": "output"
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220 },
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221 "refGenomeSource|ownFile": {
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222 "id": 3,
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223 "output_name": "output"
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224 },
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225 "singlePaired|input2": {
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226 "id": 1,
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227 "output_name": "output"
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228 },
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229 "singlePaired|pParams|own_junctions|gene_model_ann|gene_annotation_model": {
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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230 "id": 2,
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231 "output_name": "output"
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232 }
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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233 },
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265 "uuid": "None",
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266 "workflow_outputs": [
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267 {
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269 "output_name": "deletions",
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271 },
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274 "output_name": "insertions",
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276 },
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277 {
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279 "output_name": "accepted_hits",
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280 "uuid": "bb092754-4a16-42c5-a41c-60473fe7a636"
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281 },
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282 {
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283 "label": null,
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284 "output_name": "junctions",
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285 "uuid": "d20c96cf-7e14-4dc3-88ad-8059ea05cd62"
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286 }
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287 ]
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288 },
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289 "6": {
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290 "annotation": "",
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291 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1",
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292 "id": 6,
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293 "input_connections": {
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294 "guided_junctions": {
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295 "id": 5,
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296 "output_name": "junctions"
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297 },
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298 "input_bed": {
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299 "id": 4,
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300 "output_name": "junctions"
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301 }
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302 },
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303 "inputs": [],
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304 "label": null,
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galaxyp
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305 "name": "Filter BED on splice junctions",
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306 "outputs": [
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galaxyp
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307 {
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308 "name": "novel_junctions",
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309 "type": "bed"
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315 },
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317 "HideDatasetActionnovel_junctions": {
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318 "action_arguments": {},
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319 "action_type": "HideDatasetAction",
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320 "output_name": "novel_junctions"
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321 }
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322 },
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323 "tool_errors": null,
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324 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1",
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326 "tool_version": "0.0.1",
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327 "type": "tool",
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328 "uuid": "None",
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329 "workflow_outputs": []
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330 },
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331 "7": {
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332 "annotation": "",
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333 "content_id": "Extract genomic DNA 1",
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334 "id": 7,
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335 "input_connections": {
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336 "input": {
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337 "id": 6,
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338 "output_name": "novel_junctions"
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339 },
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340 "seq_source|ref_file": {
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341 "id": 3,
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342 "output_name": "output"
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343 }
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344 },
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345 "inputs": [],
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346 "label": null,
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347 "name": "Extract Genomic DNA",
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348 "outputs": [
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349 {
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350 "name": "out_file1",
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351 "type": "input"
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352 }
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353 ],
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354 "position": {
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355 "left": 1213,
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357 },
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358 "post_job_actions": {},
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359 "tool_errors": null,
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360 "tool_id": "Extract genomic DNA 1",
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361 "tool_state": "{\"out_format\": \"\\\"interval\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"__current_case__\\\": 1}\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCh37_canon.len\\\"\"}",
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362 "tool_version": "2.2.3",
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363 "type": "tool",
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364 "uuid": "None",
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365 "workflow_outputs": [
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366 {
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367 "label": null,
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368 "output_name": "out_file1",
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369 "uuid": "fd68649b-1a31-4fb1-885a-92f374e4430f"
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370 }
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371 ]
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372 },
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373 "8": {
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374 "annotation": "Set the ID prefix for generated IDs when you intend to merge multiple samples from multiple fastq inputs to guarantee unique protein junction names.",
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375 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed_sequences/translate_bed_sequences/0.1.0",
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376 "id": 8,
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377 "input_connections": {
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378 "input": {
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379 "id": 7,
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380 "output_name": "out_file1"
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381 }
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382 },
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383 "inputs": [
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384 {
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
385 "description": "runtime parameter for tool Translate BED Sequences",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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386 "name": "filter"
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
387 },
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
388 {
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
389 "description": "runtime parameter for tool Translate BED Sequences",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
390 "name": "filter"
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
391 }
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
392 ],
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
393 "label": null,
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
394 "name": "Translate BED Sequences",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
395 "outputs": [
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
396 {
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
397 "name": "translated_bed",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
398 "type": "bed"
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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399 },
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
400 {
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
401 "name": "output",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
402 "type": "fasta"
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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403 }
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
404 ],
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
405 "position": {
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
406 "left": 1431.5,
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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diff changeset
407 "top": 451.5
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
408 },
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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409 "post_job_actions": {},
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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410 "tool_errors": null,
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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411 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed_sequences/translate_bed_sequences/0.1.0",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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412 "tool_state": "{\"trim\": \"{\\\"trimseqs\\\": \\\"yes\\\", \\\"__current_case__\\\": 1}\", \"min_length\": \"\\\"\\\"\", \"fa_sep\": \"\\\"\\\"\", \"fa_db\": \"\\\"generic\\\"\", \"reference\": \"\\\"\\\"\", \"__page__\": 0, \"refsource\": \"\\\"Ensembl\\\"\", \"__rerun_remap_job_id__\": null, \"filter\": \"{\\\"filterseqs\\\": \\\"yes\\\", \\\"trailing_bp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"leading_bp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"score_name\": \"\\\"depth\\\"\", \"id_prefix\": \"\\\"\\\"\", \"input\": \"null\", \"seqtype\": \"\\\"pep:splice\\\"\"}",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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413 "tool_version": "0.1.0",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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414 "type": "tool",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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diff changeset
415 "uuid": "f6a04b0d-c01d-4b80-b66b-0a9e540b7cde",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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416 "workflow_outputs": [
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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417 {
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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418 "label": null,
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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419 "output_name": "translated_bed",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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420 "uuid": "f3c4f84f-3ce8-49cc-b932-f0122d1e6f2f"
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents:
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421 },
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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422 {
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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423 "label": null,
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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424 "output_name": "output",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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425 "uuid": "b771a5d3-fc36-4006-a967-3de09d08f3fb"
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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426 }
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents:
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427 ]
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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428 }
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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429 },
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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430 "uuid": "e0cf1a1d-4678-47cd-af5d-e2896c27e35f"
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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431 }