Mercurial > repos > jpayne > snp_pipeline

annotate CFSAN_SNP_Pipeline.ga @ 58:d53281e6edae

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author jpayne
date Mon, 17 Jun 2024 02:57:10 -0400
parents eefdd97a6749
children
rev   line source
jpayne@0 1 {
jpayne@0 2 "a_galaxy_workflow": "true",
jpayne@0 3 "annotation": "",
jpayne@0 4 "format-version": "0.1",
jpayne@0 5 "name": "CFSAN SNP Pipeline",
jpayne@0 6 "steps": {
jpayne@0 7 "0": {
jpayne@0 8 "annotation": "",
jpayne@0 9 "content_id": null,
jpayne@0 10 "errors": null,
jpayne@0 11 "id": 0,
jpayne@0 12 "input_connections": {},
jpayne@0 13 "inputs": [],
jpayne@0 14 "label": "Reference FASTA",
jpayne@0 15 "name": "Input dataset",
jpayne@0 16 "outputs": [],
jpayne@0 17 "position": {
jpayne@0 18 "left": 241.5,
jpayne@0 19 "top": 381
jpayne@0 20 },
jpayne@0 21 "tool_id": null,
jpayne@0 22 "tool_state": "{}",
jpayne@0 23 "tool_version": null,
jpayne@0 24 "type": "data_input",
jpayne@0 25 "uuid": "024fcab7-2daf-4b89-9730-614ee2737db8",
jpayne@0 26 "workflow_outputs": [
jpayne@0 27 {
jpayne@0 28 "label": null,
jpayne@0 29 "output_name": "output",
jpayne@0 30 "uuid": "87db8281-092f-4f81-be41-152af355ebd6"
jpayne@0 31 }
jpayne@0 32 ]
jpayne@0 33 },
jpayne@0 34 "1": {
jpayne@0 35 "annotation": "",
jpayne@0 36 "content_id": null,
jpayne@0 37 "errors": null,
jpayne@0 38 "id": 1,
jpayne@0 39 "input_connections": {},
jpayne@0 40 "inputs": [],
jpayne@0 41 "label": "Collection of Paired-End Reads",
jpayne@0 42 "name": "Input dataset collection",
jpayne@0 43 "outputs": [],
jpayne@0 44 "position": {
jpayne@0 45 "left": 222,
jpayne@0 46 "top": 746
jpayne@0 47 },
jpayne@0 48 "tool_id": null,
jpayne@0 49 "tool_state": "{\"collection_type\": \"list:paired\"}",
jpayne@0 50 "tool_version": null,
jpayne@0 51 "type": "data_collection_input",
jpayne@0 52 "uuid": "66a18e16-33f7-4488-ac17-508725a58279",
jpayne@0 53 "workflow_outputs": [
jpayne@0 54 {
jpayne@0 55 "label": null,
jpayne@0 56 "output_name": "output",
jpayne@0 57 "uuid": "1a3c2f8a-e443-44cc-8490-35ebb5a9ebc4"
jpayne@0 58 }
jpayne@0 59 ]
jpayne@0 60 },
jpayne@0 61 "2": {
jpayne@0 62 "annotation": "",
jpayne@0 63 "content_id": "map_reads",
jpayne@0 64 "errors": null,
jpayne@0 65 "id": 2,
jpayne@0 66 "input_connections": {
jpayne@0 67 "reads|coll": {
jpayne@0 68 "id": 1,
jpayne@0 69 "output_name": "output"
jpayne@0 70 },
jpayne@0 71 "source|reference": {
jpayne@0 72 "id": 0,
jpayne@0 73 "output_name": "output"
jpayne@0 74 }
jpayne@0 75 },
jpayne@0 76 "inputs": [
jpayne@0 77 {
jpayne@0 78 "description": "runtime parameter for tool 1. Map Reads",
jpayne@0 79 "name": "source"
jpayne@0 80 },
jpayne@0 81 {
jpayne@0 82 "description": "runtime parameter for tool 1. Map Reads",
jpayne@0 83 "name": "reads"
jpayne@0 84 }
jpayne@0 85 ],
jpayne@0 86 "label": null,
jpayne@0 87 "name": "1. Map Reads",
jpayne@0 88 "outputs": [
jpayne@0 89 {
jpayne@0 90 "name": "align_from_collection",
jpayne@0 91 "type": "sam"
jpayne@0 92 },
jpayne@0 93 {
jpayne@0 94 "name": "align_from_history",
jpayne@0 95 "type": "sam"
jpayne@0 96 },
jpayne@0 97 {
jpayne@0 98 "name": "cache_log",
jpayne@0 99 "type": "txt"
jpayne@0 100 },
jpayne@0 101 {
jpayne@0 102 "name": "ref_out",
jpayne@0 103 "type": "fasta"
jpayne@0 104 }
jpayne@0 105 ],
jpayne@0 106 "position": {
jpayne@0 107 "left": 505.5,
jpayne@0 108 "top": 536.5
jpayne@0 109 },
jpayne@0 110 "post_job_actions": {},
jpayne@0 111 "tool_id": "map_reads",
jpayne@0 112 "tool_state": "{\"source\": \"{\\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"source_select\\\": \\\"history\\\"}\", \"reads\": \"{\\\"coll\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"reads_select\\\": \\\"collection\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
jpayne@0 113 "tool_version": "1.0.1",
jpayne@0 114 "type": "tool",
jpayne@0 115 "uuid": "112e11d9-2670-4aae-9bee-3b25e0dd3398",
jpayne@0 116 "workflow_outputs": []
jpayne@0 117 },
jpayne@0 118 "3": {
jpayne@0 119 "annotation": "",
jpayne@0 120 "content_id": "call_sites",
jpayne@0 121 "errors": null,
jpayne@0 122 "id": 3,
jpayne@0 123 "input_connections": {
jpayne@0 124 "input": {
jpayne@0 125 "id": 0,
jpayne@0 126 "output_name": "output"
jpayne@0 127 },
jpayne@0 128 "sample": {
jpayne@0 129 "id": 2,
jpayne@0 130 "output_name": "align_from_collection"
jpayne@0 131 }
jpayne@0 132 },
jpayne@0 133 "inputs": [],
jpayne@0 134 "label": null,
jpayne@0 135 "name": "2. Call Sites",
jpayne@0 136 "outputs": [
jpayne@0 137 {
jpayne@0 138 "name": "calls",
jpayne@0 139 "type": "vcf"
jpayne@0 140 },
jpayne@0 141 {
jpayne@0 142 "name": "pileup",
jpayne@0 143 "type": "pileup"
jpayne@0 144 },
jpayne@0 145 {
jpayne@0 146 "name": "metrics",
jpayne@0 147 "type": "txt"
jpayne@0 148 },
jpayne@0 149 {
jpayne@0 150 "name": "cache_log",
jpayne@0 151 "type": "txt"
jpayne@0 152 }
jpayne@0 153 ],
jpayne@0 154 "position": {
jpayne@0 155 "left": 915.5,
jpayne@0 156 "top": 536.5
jpayne@0 157 },
jpayne@0 158 "post_job_actions": {},
jpayne@0 159 "tool_id": "call_sites",
jpayne@0 160 "tool_state": "{\"sample\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 24}]}\", \"input\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 26}]}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
jpayne@0 161 "tool_version": "1.0.1",
jpayne@0 162 "type": "tool",
jpayne@0 163 "uuid": "23b2c1b4-f213-41a2-ad71-6a2c579ac36b",
jpayne@0 164 "workflow_outputs": []
jpayne@0 165 },
jpayne@0 166 "4": {
jpayne@0 167 "annotation": "",
jpayne@0 168 "content_id": "filter_regions",
jpayne@0 169 "errors": null,
jpayne@0 170 "id": 4,
jpayne@0 171 "input_connections": {
jpayne@0 172 "calls": {
jpayne@0 173 "id": 3,
jpayne@0 174 "output_name": "calls"
jpayne@0 175 },
jpayne@0 176 "reference": {
jpayne@0 177 "id": 0,
jpayne@0 178 "output_name": "output"
jpayne@0 179 }
jpayne@0 180 },
jpayne@0 181 "inputs": [],
jpayne@0 182 "label": null,
jpayne@0 183 "name": "3. Filter SNP Regions",
jpayne@0 184 "outputs": [
jpayne@0 185 {
jpayne@0 186 "name": "filcalls",
jpayne@0 187 "type": "vcf"
jpayne@0 188 },
jpayne@0 189 {
jpayne@0 190 "name": "excludes",
jpayne@0 191 "type": "vcf"
jpayne@0 192 }
jpayne@0 193 ],
jpayne@0 194 "position": {
jpayne@0 195 "left": 1231,
jpayne@0 196 "top": 304.5
jpayne@0 197 },
jpayne@0 198 "post_job_actions": {},
jpayne@0 199 "tool_id": "filter_regions",
jpayne@0 200 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"reference\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 26}]}\", \"calls\": \"null\"}",
jpayne@0 201 "tool_version": "1.0.1",
jpayne@0 202 "type": "tool",
jpayne@0 203 "uuid": "b2f3ecfe-ecdb-4014-a362-78f35426559f",
jpayne@0 204 "workflow_outputs": []
jpayne@0 205 },
jpayne@0 206 "5": {
jpayne@0 207 "annotation": "",
jpayne@0 208 "content_id": "merge_sites",
jpayne@0 209 "errors": null,
jpayne@0 210 "id": 5,
jpayne@0 211 "input_connections": {
jpayne@0 212 "calls": {
jpayne@0 213 "id": 3,
jpayne@0 214 "output_name": "calls"
jpayne@0 215 }
jpayne@0 216 },
jpayne@0 217 "inputs": [
jpayne@0 218 {
jpayne@0 219 "description": "runtime parameter for tool 4. Merge Sites",
jpayne@0 220 "name": "calls"
jpayne@0 221 }
jpayne@0 222 ],
jpayne@0 223 "label": null,
jpayne@0 224 "name": "4. Merge Sites",
jpayne@0 225 "outputs": [
jpayne@0 226 {
jpayne@0 227 "name": "snplist",
jpayne@0 228 "type": "txt"
jpayne@0 229 }
jpayne@0 230 ],
jpayne@0 231 "position": {
jpayne@0 232 "left": 1535.5,
jpayne@0 233 "top": 717
jpayne@0 234 },
jpayne@0 235 "post_job_actions": {
jpayne@0 236 "TagDatasetActionsnplist": {
jpayne@0 237 "action_arguments": {
jpayne@0 238 "tags": "unfiltered"
jpayne@0 239 },
jpayne@0 240 "action_type": "TagDatasetAction",
jpayne@0 241 "output_name": "snplist"
jpayne@0 242 }
jpayne@0 243 },
jpayne@0 244 "tool_id": "merge_sites",
jpayne@0 245 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"calls\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
jpayne@0 246 "tool_version": "1.0.1",
jpayne@0 247 "type": "tool",
jpayne@0 248 "uuid": "012268fa-41bf-4227-b812-47009b8315c3",
jpayne@0 249 "workflow_outputs": [
jpayne@0 250 {
jpayne@0 251 "label": "Unfiltered SNP list",
jpayne@0 252 "output_name": "snplist",
jpayne@0 253 "uuid": "0dd22e5c-15b8-4772-8304-a81d3de1bee4"
jpayne@0 254 }
jpayne@0 255 ]
jpayne@0 256 },
jpayne@0 257 "6": {
jpayne@0 258 "annotation": "",
jpayne@0 259 "content_id": "merge_sites",
jpayne@0 260 "errors": null,
jpayne@0 261 "id": 6,
jpayne@0 262 "input_connections": {
jpayne@0 263 "calls": {
jpayne@0 264 "id": 4,
jpayne@0 265 "output_name": "filcalls"
jpayne@0 266 }
jpayne@0 267 },
jpayne@0 268 "inputs": [
jpayne@0 269 {
jpayne@0 270 "description": "runtime parameter for tool 4. Merge Sites",
jpayne@0 271 "name": "calls"
jpayne@0 272 }
jpayne@0 273 ],
jpayne@0 274 "label": null,
jpayne@0 275 "name": "4. Merge Sites",
jpayne@0 276 "outputs": [
jpayne@0 277 {
jpayne@0 278 "name": "snplist",
jpayne@0 279 "type": "txt"
jpayne@0 280 }
jpayne@0 281 ],
jpayne@0 282 "position": {
jpayne@0 283 "left": 1530.5,
jpayne@0 284 "top": 299
jpayne@0 285 },
jpayne@0 286 "post_job_actions": {
jpayne@0 287 "TagDatasetActionsnplist": {
jpayne@0 288 "action_arguments": {
jpayne@0 289 "tags": "filtered"
jpayne@0 290 },
jpayne@0 291 "action_type": "TagDatasetAction",
jpayne@0 292 "output_name": "snplist"
jpayne@0 293 }
jpayne@0 294 },
jpayne@0 295 "tool_id": "merge_sites",
jpayne@0 296 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"calls\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
jpayne@0 297 "tool_version": "1.0.1",
jpayne@0 298 "type": "tool",
jpayne@0 299 "uuid": "bb0d410f-4d22-400e-8dc2-ddf62027ca3d",
jpayne@0 300 "workflow_outputs": [
jpayne@0 301 {
jpayne@0 302 "label": "Filtered SNP list",
jpayne@0 303 "output_name": "snplist",
jpayne@0 304 "uuid": "ab240b50-625d-4468-90fe-02363974abea"
jpayne@0 305 }
jpayne@0 306 ]
jpayne@0 307 },
jpayne@0 308 "7": {
jpayne@0 309 "annotation": "",
jpayne@0 310 "content_id": "call_consensus",
jpayne@0 311 "errors": null,
jpayne@0 312 "id": 7,
jpayne@0 313 "input_connections": {
jpayne@0 314 "call_pileup": {
jpayne@0 315 "id": 3,
jpayne@0 316 "output_name": "pileup"
jpayne@0 317 },
jpayne@0 318 "calls": {
jpayne@0 319 "id": 3,
jpayne@0 320 "output_name": "calls"
jpayne@0 321 },
jpayne@0 322 "snps": {
jpayne@0 323 "id": 5,
jpayne@0 324 "output_name": "snplist"
jpayne@0 325 }
jpayne@0 326 },
jpayne@0 327 "inputs": [],
jpayne@0 328 "label": null,
jpayne@0 329 "name": "5. Call consensus SNPs",
jpayne@0 330 "outputs": [
jpayne@0 331 {
jpayne@0 332 "name": "calls_consensus_vcf",
jpayne@0 333 "type": "vcf"
jpayne@0 334 },
jpayne@0 335 {
jpayne@0 336 "name": "calls_consensus_fa",
jpayne@0 337 "type": "fasta"
jpayne@0 338 },
jpayne@0 339 {
jpayne@0 340 "name": "cache_log",
jpayne@0 341 "type": "txt"
jpayne@0 342 }
jpayne@0 343 ],
jpayne@0 344 "position": {
jpayne@0 345 "left": 1748.5,
jpayne@0 346 "top": 707.5
jpayne@0 347 },
jpayne@0 348 "post_job_actions": {},
jpayne@0 349 "tool_id": "call_consensus",
jpayne@0 350 "tool_state": "{\"snps\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 26}]}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"call_pileup\": \"null\", \"calls\": \"null\"}",
jpayne@0 351 "tool_version": "1.0.1",
jpayne@0 352 "type": "tool",
jpayne@0 353 "uuid": "8785777e-c7c0-4416-8c5c-5201d218fa71",
jpayne@0 354 "workflow_outputs": []
jpayne@0 355 },
jpayne@0 356 "8": {
jpayne@0 357 "annotation": "",
jpayne@0 358 "content_id": "call_consensus",
jpayne@0 359 "errors": null,
jpayne@0 360 "id": 8,
jpayne@0 361 "input_connections": {
jpayne@0 362 "call_pileup": {
jpayne@0 363 "id": 3,
jpayne@0 364 "output_name": "pileup"
jpayne@0 365 },
jpayne@0 366 "calls": {
jpayne@0 367 "id": 4,
jpayne@0 368 "output_name": "filcalls"
jpayne@0 369 },
jpayne@0 370 "snps": {
jpayne@0 371 "id": 6,
jpayne@0 372 "output_name": "snplist"
jpayne@0 373 }
jpayne@0 374 },
jpayne@0 375 "inputs": [],
jpayne@0 376 "label": null,
jpayne@0 377 "name": "5. Call consensus SNPs",
jpayne@0 378 "outputs": [
jpayne@0 379 {
jpayne@0 380 "name": "calls_consensus_vcf",
jpayne@0 381 "type": "vcf"
jpayne@0 382 },
jpayne@0 383 {
jpayne@0 384 "name": "calls_consensus_fa",
jpayne@0 385 "type": "fasta"
jpayne@0 386 },
jpayne@0 387 {
jpayne@0 388 "name": "cache_log",
jpayne@0 389 "type": "txt"
jpayne@0 390 }
jpayne@0 391 ],
jpayne@0 392 "position": {
jpayne@0 393 "left": 1752.5,
jpayne@0 394 "top": 289.5
jpayne@0 395 },
jpayne@0 396 "post_job_actions": {},
jpayne@0 397 "tool_id": "call_consensus",
jpayne@0 398 "tool_state": "{\"snps\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 26}]}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"call_pileup\": \"null\", \"calls\": \"null\"}",
jpayne@0 399 "tool_version": "1.0.1",
jpayne@0 400 "type": "tool",
jpayne@0 401 "uuid": "14dbd077-15fc-4dbe-8883-b6184d696428",
jpayne@0 402 "workflow_outputs": []
jpayne@0 403 },
jpayne@0 404 "9": {
jpayne@0 405 "annotation": "",
jpayne@0 406 "content_id": "merge_vcfs",
jpayne@0 407 "errors": null,
jpayne@0 408 "id": 9,
jpayne@0 409 "input_connections": {
jpayne@0 410 "vcfs": {
jpayne@0 411 "id": 7,
jpayne@0 412 "output_name": "calls_consensus_vcf"
jpayne@0 413 }
jpayne@0 414 },
jpayne@0 415 "inputs": [
jpayne@0 416 {
jpayne@0 417 "description": "runtime parameter for tool 6. Merge VCFs",
jpayne@0 418 "name": "vcfs"
jpayne@0 419 }
jpayne@0 420 ],
jpayne@0 421 "label": null,
jpayne@0 422 "name": "6. Merge VCFs",
jpayne@0 423 "outputs": [
jpayne@0 424 {
jpayne@0 425 "name": "snpmav",
jpayne@0 426 "type": "vcf"
jpayne@0 427 }
jpayne@0 428 ],
jpayne@0 429 "position": {
jpayne@0 430 "left": 2050.5,
jpayne@0 431 "top": 644
jpayne@0 432 },
jpayne@0 433 "post_job_actions": {
jpayne@0 434 "TagDatasetActionsnpmav": {
jpayne@0 435 "action_arguments": {
jpayne@0 436 "tags": "unfiltered"
jpayne@0 437 },
jpayne@0 438 "action_type": "TagDatasetAction",
jpayne@0 439 "output_name": "snpmav"
jpayne@0 440 }
jpayne@0 441 },
jpayne@0 442 "tool_id": "merge_vcfs",
jpayne@0 443 "tool_state": "{\"vcfs\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
jpayne@0 444 "tool_version": "1.0.1",
jpayne@0 445 "type": "tool",
jpayne@0 446 "uuid": "37131dc0-b85a-4f76-9bfc-96d1ce05f485",
jpayne@0 447 "workflow_outputs": [
jpayne@0 448 {
jpayne@0 449 "label": "Unfiltered SNP matrix (VCF)",
jpayne@0 450 "output_name": "snpmav",
jpayne@0 451 "uuid": "4cf3ea09-55ae-4656-abc7-9e0ae6f96a3e"
jpayne@0 452 }
jpayne@0 453 ]
jpayne@0 454 },
jpayne@0 455 "10": {
jpayne@0 456 "annotation": "",
jpayne@0 457 "content_id": "snp_matrix",
jpayne@0 458 "errors": null,
jpayne@0 459 "id": 10,
jpayne@0 460 "input_connections": {
jpayne@0 461 "cons": {
jpayne@0 462 "id": 7,
jpayne@0 463 "output_name": "calls_consensus_fa"
jpayne@0 464 },
jpayne@0 465 "reference|reference": {
jpayne@0 466 "id": 0,
jpayne@0 467 "output_name": "output"
jpayne@0 468 },
jpayne@0 469 "snplist": {
jpayne@0 470 "id": 5,
jpayne@0 471 "output_name": "snplist"
jpayne@0 472 }
jpayne@0 473 },
jpayne@0 474 "inputs": [
jpayne@0 475 {
jpayne@0 476 "description": "runtime parameter for tool 7. Create a SNP matrix",
jpayne@0 477 "name": "snplist"
jpayne@0 478 },
jpayne@0 479 {
jpayne@0 480 "description": "runtime parameter for tool 7. Create a SNP matrix",
jpayne@0 481 "name": "cons"
jpayne@0 482 },
jpayne@0 483 {
jpayne@0 484 "description": "runtime parameter for tool 7. Create a SNP matrix",
jpayne@0 485 "name": "reference"
jpayne@0 486 }
jpayne@0 487 ],
jpayne@0 488 "label": null,
jpayne@0 489 "name": "7. Create a SNP matrix",
jpayne@0 490 "outputs": [
jpayne@0 491 {
jpayne@0 492 "name": "snpma",
jpayne@0 493 "type": "fasta"
jpayne@0 494 },
jpayne@0 495 {
jpayne@0 496 "name": "pairws",
jpayne@0 497 "type": "tsv"
jpayne@0 498 },
jpayne@0 499 {
jpayne@0 500 "name": "distma",
jpayne@0 501 "type": "tsv"
jpayne@0 502 },
jpayne@0 503 {
jpayne@0 504 "name": "referenceSNP",
jpayne@0 505 "type": "fasta"
jpayne@0 506 },
jpayne@0 507 {
jpayne@0 508 "name": "metrics",
jpayne@0 509 "type": "tsv"
jpayne@0 510 }
jpayne@0 511 ],
jpayne@0 512 "position": {
jpayne@0 513 "left": 2053,
jpayne@0 514 "top": 784
jpayne@0 515 },
jpayne@0 516 "post_job_actions": {
jpayne@0 517 "HideDatasetActionmetrics": {
jpayne@0 518 "action_arguments": {},
jpayne@0 519 "action_type": "HideDatasetAction",
jpayne@0 520 "output_name": "metrics"
jpayne@0 521 },
jpayne@0 522 "TagDatasetActiondistma": {
jpayne@0 523 "action_arguments": {
jpayne@0 524 "tags": "unfiltered"
jpayne@0 525 },
jpayne@0 526 "action_type": "TagDatasetAction",
jpayne@0 527 "output_name": "distma"
jpayne@0 528 },
jpayne@0 529 "TagDatasetActionreferenceSNP": {
jpayne@0 530 "action_arguments": {
jpayne@0 531 "tags": "unfiltered"
jpayne@0 532 },
jpayne@0 533 "action_type": "TagDatasetAction",
jpayne@0 534 "output_name": "referenceSNP"
jpayne@0 535 },
jpayne@0 536 "TagDatasetActionsnpma": {
jpayne@0 537 "action_arguments": {
jpayne@0 538 "tags": "unfiltered"
jpayne@0 539 },
jpayne@0 540 "action_type": "TagDatasetAction",
jpayne@0 541 "output_name": "snpma"
jpayne@0 542 }
jpayne@0 543 },
jpayne@0 544 "tool_id": "snp_matrix",
jpayne@0 545 "tool_state": "{\"__page__\": null, \"snplist\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"cons\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"reference\": \"{\\\"ref\\\": \\\"history\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\"}",
jpayne@0 546 "tool_version": "1.0.1",
jpayne@0 547 "type": "tool",
jpayne@0 548 "uuid": "22e52e86-ab1d-4201-9850-86d4bc0a8110",
jpayne@0 549 "workflow_outputs": [
jpayne@0 550 {
jpayne@0 551 "label": "Unfiltered SNP distance matrix",
jpayne@0 552 "output_name": "distma",
jpayne@0 553 "uuid": "c8e44902-b18f-45d5-9aa6-81471cfcd73d"
jpayne@0 554 },
jpayne@0 555 {
jpayne@0 556 "label": "Unfiltered SNP reference (FASTA)",
jpayne@0 557 "output_name": "referenceSNP",
jpayne@0 558 "uuid": "b60c56cf-c9df-4eef-85d0-39717232aef0"
jpayne@0 559 },
jpayne@0 560 {
jpayne@0 561 "label": "Unfiltered SNP matrix (FASTA)",
jpayne@0 562 "output_name": "snpma",
jpayne@0 563 "uuid": "07789496-d5db-48ec-98ad-0c25f5e93fcc"
jpayne@0 564 },
jpayne@0 565 {
jpayne@0 566 "label": "Unfiltered pairwise SNP distance table",
jpayne@0 567 "output_name": "pairws",
jpayne@0 568 "uuid": "e34a6bc0-7165-4444-ae06-e7679248b6bf"
jpayne@0 569 }
jpayne@0 570 ]
jpayne@0 571 },
jpayne@0 572 "11": {
jpayne@0 573 "annotation": "",
jpayne@0 574 "content_id": "merge_vcfs",
jpayne@0 575 "errors": null,
jpayne@0 576 "id": 11,
jpayne@0 577 "input_connections": {
jpayne@0 578 "vcfs": {
jpayne@0 579 "id": 8,
jpayne@0 580 "output_name": "calls_consensus_vcf"
jpayne@0 581 }
jpayne@0 582 },
jpayne@0 583 "inputs": [
jpayne@0 584 {
jpayne@0 585 "description": "runtime parameter for tool 6. Merge VCFs",
jpayne@0 586 "name": "vcfs"
jpayne@0 587 }
jpayne@0 588 ],
jpayne@0 589 "label": null,
jpayne@0 590 "name": "6. Merge VCFs",
jpayne@0 591 "outputs": [
jpayne@0 592 {
jpayne@0 593 "name": "snpmav",
jpayne@0 594 "type": "vcf"
jpayne@0 595 }
jpayne@0 596 ],
jpayne@0 597 "position": {
jpayne@0 598 "left": 2054.5,
jpayne@0 599 "top": 227
jpayne@0 600 },
jpayne@0 601 "post_job_actions": {
jpayne@0 602 "TagDatasetActionsnpmav": {
jpayne@0 603 "action_arguments": {
jpayne@0 604 "tags": "filtered"
jpayne@0 605 },
jpayne@0 606 "action_type": "TagDatasetAction",
jpayne@0 607 "output_name": "snpmav"
jpayne@0 608 }
jpayne@0 609 },
jpayne@0 610 "tool_id": "merge_vcfs",
jpayne@0 611 "tool_state": "{\"vcfs\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
jpayne@0 612 "tool_version": "1.0.1",
jpayne@0 613 "type": "tool",
jpayne@0 614 "uuid": "55024e57-310a-4ab7-927b-034c78b757d9",
jpayne@0 615 "workflow_outputs": [
jpayne@0 616 {
jpayne@0 617 "label": "Filtered SNP matrix (VCF)",
jpayne@0 618 "output_name": "snpmav",
jpayne@0 619 "uuid": "b4118679-e622-4a93-8a15-aaab125c2475"
jpayne@0 620 }
jpayne@0 621 ]
jpayne@0 622 },
jpayne@0 623 "12": {
jpayne@0 624 "annotation": "",
jpayne@0 625 "content_id": "snp_matrix",
jpayne@0 626 "errors": null,
jpayne@0 627 "id": 12,
jpayne@0 628 "input_connections": {
jpayne@0 629 "cons": {
jpayne@0 630 "id": 8,
jpayne@0 631 "output_name": "calls_consensus_fa"
jpayne@0 632 },
jpayne@0 633 "reference|reference": {
jpayne@0 634 "id": 0,
jpayne@0 635 "output_name": "output"
jpayne@0 636 },
jpayne@0 637 "snplist": {
jpayne@0 638 "id": 6,
jpayne@0 639 "output_name": "snplist"
jpayne@0 640 }
jpayne@0 641 },
jpayne@0 642 "inputs": [
jpayne@0 643 {
jpayne@0 644 "description": "runtime parameter for tool 7. Create a SNP matrix",
jpayne@0 645 "name": "snplist"
jpayne@0 646 },
jpayne@0 647 {
jpayne@0 648 "description": "runtime parameter for tool 7. Create a SNP matrix",
jpayne@0 649 "name": "cons"
jpayne@0 650 },
jpayne@0 651 {
jpayne@0 652 "description": "runtime parameter for tool 7. Create a SNP matrix",
jpayne@0 653 "name": "reference"
jpayne@0 654 }
jpayne@0 655 ],
jpayne@0 656 "label": null,
jpayne@0 657 "name": "7. Create a SNP matrix",
jpayne@0 658 "outputs": [
jpayne@0 659 {
jpayne@0 660 "name": "snpma",
jpayne@0 661 "type": "fasta"
jpayne@0 662 },
jpayne@0 663 {
jpayne@0 664 "name": "pairws",
jpayne@0 665 "type": "tsv"
jpayne@0 666 },
jpayne@0 667 {
jpayne@0 668 "name": "distma",
jpayne@0 669 "type": "tsv"
jpayne@0 670 },
jpayne@0 671 {
jpayne@0 672 "name": "referenceSNP",
jpayne@0 673 "type": "fasta"
jpayne@0 674 },
jpayne@0 675 {
jpayne@0 676 "name": "metrics",
jpayne@0 677 "type": "tsv"
jpayne@0 678 }
jpayne@0 679 ],
jpayne@0 680 "position": {
jpayne@0 681 "left": 2050,
jpayne@0 682 "top": 349
jpayne@0 683 },
jpayne@0 684 "post_job_actions": {
jpayne@0 685 "HideDatasetActionmetrics": {
jpayne@0 686 "action_arguments": {},
jpayne@0 687 "action_type": "HideDatasetAction",
jpayne@0 688 "output_name": "metrics"
jpayne@0 689 },
jpayne@0 690 "TagDatasetActiondistma": {
jpayne@0 691 "action_arguments": {
jpayne@0 692 "tags": "filtered"
jpayne@0 693 },
jpayne@0 694 "action_type": "TagDatasetAction",
jpayne@0 695 "output_name": "distma"
jpayne@0 696 },
jpayne@0 697 "TagDatasetActionpairws": {
jpayne@0 698 "action_arguments": {
jpayne@0 699 "tags": "filtered"
jpayne@0 700 },
jpayne@0 701 "action_type": "TagDatasetAction",
jpayne@0 702 "output_name": "pairws"
jpayne@0 703 },
jpayne@0 704 "TagDatasetActionreferenceSNP": {
jpayne@0 705 "action_arguments": {
jpayne@0 706 "tags": "filtered"
jpayne@0 707 },
jpayne@0 708 "action_type": "TagDatasetAction",
jpayne@0 709 "output_name": "referenceSNP"
jpayne@0 710 },
jpayne@0 711 "TagDatasetActionsnpma": {
jpayne@0 712 "action_arguments": {
jpayne@0 713 "tags": "filtered"
jpayne@0 714 },
jpayne@0 715 "action_type": "TagDatasetAction",
jpayne@0 716 "output_name": "snpma"
jpayne@0 717 }
jpayne@0 718 },
jpayne@0 719 "tool_id": "snp_matrix",
jpayne@0 720 "tool_state": "{\"__page__\": null, \"snplist\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"cons\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"reference\": \"{\\\"ref\\\": \\\"history\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\"}",
jpayne@0 721 "tool_version": "1.0.1",
jpayne@0 722 "type": "tool",
jpayne@0 723 "uuid": "6d0adb1c-637a-436a-aa32-64cb54b414f6",
jpayne@0 724 "workflow_outputs": [
jpayne@0 725 {
jpayne@0 726 "label": "Filtered SNP distance matrix",
jpayne@0 727 "output_name": "distma",
jpayne@0 728 "uuid": "0b3437f6-5370-415c-bd02-f85fd4527783"
jpayne@0 729 },
jpayne@0 730 {
jpayne@0 731 "label": "Filtered SNP reference (FASTA)",
jpayne@0 732 "output_name": "referenceSNP",
jpayne@0 733 "uuid": "bca4048e-2af1-4764-a1de-cf987914fc2a"
jpayne@0 734 },
jpayne@0 735 {
jpayne@0 736 "label": "Filtered SNP matrix (FASTA)",
jpayne@0 737 "output_name": "snpma",
jpayne@0 738 "uuid": "2ca775f1-917f-4824-b11a-1506c2e75bc6"
jpayne@0 739 },
jpayne@0 740 {
jpayne@0 741 "label": "Filtered pairwise SNP distance table",
jpayne@0 742 "output_name": "pairws",
jpayne@0 743 "uuid": "6d385865-e585-4bc1-956f-95110edf6095"
jpayne@0 744 }
jpayne@0 745 ]
jpayne@0 746 }
jpayne@0 747 },
jpayne@0 748 "tags": [],
jpayne@0 749 "uuid": "304cdcb3-78a5-43bf-be17-c0824e30e02c"
jpayne@0 750 }