Mercurial > repos > chrisd > amrplusplus_workflow
comparison amrplusplus_workflow.ga @ 7:0b7210ad9187 draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
| author | chrisd |
|---|---|
| date | Sat, 25 Jun 2016 17:17:42 -0400 |
| parents | 86dc721b6860 |
| children | 0eae27b15aa0 |
comparison
equal
deleted
inserted
replaced
| 6:86dc721b6860 | 7:0b7210ad9187 |
|---|---|
| 25 "tool_errors": null, | 25 "tool_errors": null, |
| 26 "tool_id": null, | 26 "tool_id": null, |
| 27 "tool_state": "{\"name\": \"FASTQ Forward\"}", | 27 "tool_state": "{\"name\": \"FASTQ Forward\"}", |
| 28 "tool_version": null, | 28 "tool_version": null, |
| 29 "type": "data_input", | 29 "type": "data_input", |
| 30 "uuid": "9c1f5852-9697-40e2-bc6f-7ac65ad647ce", | 30 "uuid": "f1e841db-6f7a-4f32-bd87-8d0d934c4cc1", |
| 31 "workflow_outputs": [] | 31 "workflow_outputs": [ |
| 32 { | |
| 33 "label": null, | |
| 34 "output_name": "output", | |
| 35 "uuid": "ad47f164-7e7a-4d22-a967-551b2378427a" | |
| 36 } | |
| 37 ] | |
| 32 }, | 38 }, |
| 33 "1": { | 39 "1": { |
| 34 "annotation": "", | 40 "annotation": "", |
| 35 "content_id": null, | 41 "content_id": null, |
| 36 "id": 1, | 42 "id": 1, |
| 51 "tool_errors": null, | 57 "tool_errors": null, |
| 52 "tool_id": null, | 58 "tool_id": null, |
| 53 "tool_state": "{\"name\": \"FASTQ Reverse\"}", | 59 "tool_state": "{\"name\": \"FASTQ Reverse\"}", |
| 54 "tool_version": null, | 60 "tool_version": null, |
| 55 "type": "data_input", | 61 "type": "data_input", |
| 56 "uuid": "030bf3fc-ee71-46c4-bfcf-8d963c04a478", | 62 "uuid": "a24ee7c0-b919-4426-8866-7d9939536e12", |
| 57 "workflow_outputs": [] | 63 "workflow_outputs": [ |
| 64 { | |
| 65 "label": null, | |
| 66 "output_name": "output", | |
| 67 "uuid": "edba093d-cdda-4530-916e-a566d94e2040" | |
| 68 } | |
| 69 ] | |
| 58 }, | 70 }, |
| 59 "2": { | 71 "2": { |
| 60 "annotation": "", | 72 "annotation": "", |
| 61 "content_id": null, | 73 "content_id": null, |
| 62 "id": 2, | 74 "id": 2, |
| 77 "tool_errors": null, | 89 "tool_errors": null, |
| 78 "tool_id": null, | 90 "tool_id": null, |
| 79 "tool_state": "{\"name\": \"Host Genome\"}", | 91 "tool_state": "{\"name\": \"Host Genome\"}", |
| 80 "tool_version": null, | 92 "tool_version": null, |
| 81 "type": "data_input", | 93 "type": "data_input", |
| 82 "uuid": "95f884fc-215e-4d54-8212-e43be8a779b5", | 94 "uuid": "96c8f450-cb64-4641-884a-c1dabceeff5d", |
| 83 "workflow_outputs": [] | 95 "workflow_outputs": [ |
| 96 { | |
| 97 "label": null, | |
| 98 "output_name": "output", | |
| 99 "uuid": "2fb141c8-5d0b-4044-906d-adaa7a07f66e" | |
| 100 } | |
| 101 ] | |
| 84 }, | 102 }, |
| 85 "3": { | 103 "3": { |
| 86 "annotation": "", | 104 "annotation": "", |
| 87 "content_id": null, | 105 "content_id": null, |
| 88 "id": 3, | 106 "id": 3, |
| 103 "tool_errors": null, | 121 "tool_errors": null, |
| 104 "tool_id": null, | 122 "tool_id": null, |
| 105 "tool_state": "{\"name\": \"AMR Database\"}", | 123 "tool_state": "{\"name\": \"AMR Database\"}", |
| 106 "tool_version": null, | 124 "tool_version": null, |
| 107 "type": "data_input", | 125 "type": "data_input", |
| 108 "uuid": "8a65e391-b837-41ef-9575-bedf5294da9e", | 126 "uuid": "2615ede9-3d0a-422b-b04d-829157475d47", |
| 109 "workflow_outputs": [] | 127 "workflow_outputs": [ |
| 128 { | |
| 129 "label": null, | |
| 130 "output_name": "output", | |
| 131 "uuid": "32fcc9ba-8864-4fa7-a337-917a9612844a" | |
| 132 } | |
| 133 ] | |
| 110 }, | 134 }, |
| 111 "4": { | 135 "4": { |
| 112 "annotation": "", | 136 "annotation": "", |
| 113 "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", | 137 "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", |
| 114 "id": 4, | 138 "id": 4, |
| 195 "tool_shed": "toolshed.g2.bx.psu.edu" | 219 "tool_shed": "toolshed.g2.bx.psu.edu" |
| 196 }, | 220 }, |
| 197 "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"window_size\\\": \\\"4\\\", \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"__current_case__\\\": 0, \\\"required_quality\\\": \\\"20\\\"}}]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_end\": \"{\\\"is_paired_end\\\": \\\"true\\\", \\\"paired_input_type_conditional\\\": {\\\"paired_input_type\\\": \\\"pair_of_files\\\", \\\"fastq_r1_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"fastq_r2_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"__current_case__\\\": 1}\", \"illuminaclip\": \"{\\\"do_illuminaclip\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\"}", | 221 "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"window_size\\\": \\\"4\\\", \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"__current_case__\\\": 0, \\\"required_quality\\\": \\\"20\\\"}}]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_end\": \"{\\\"is_paired_end\\\": \\\"true\\\", \\\"paired_input_type_conditional\\\": {\\\"paired_input_type\\\": \\\"pair_of_files\\\", \\\"fastq_r1_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"fastq_r2_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"__current_case__\\\": 1}\", \"illuminaclip\": \"{\\\"do_illuminaclip\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\"}", |
| 198 "tool_version": "0.32.3", | 222 "tool_version": "0.32.3", |
| 199 "type": "tool", | 223 "type": "tool", |
| 200 "uuid": "0d5a87ee-c6a3-4bd1-b416-226d0e4783ab", | 224 "uuid": "c943ae63-aa6c-4d42-9088-b08335b8b6c6", |
| 201 "workflow_outputs": [ | 225 "workflow_outputs": [ |
| 202 { | 226 { |
| 203 "label": null, | 227 "label": null, |
| 204 "output_name": "fastq_out_r1_paired", | 228 "output_name": "fastq_out_r1_paired", |
| 205 "uuid": "6e06861e-a08e-4fbf-bdd6-daa51499d669" | 229 "uuid": "e5cb04a2-09b6-41e5-b93d-54c4c6c8e488" |
| 206 }, | 230 }, |
| 207 { | 231 { |
| 208 "label": null, | 232 "label": null, |
| 209 "output_name": "fastq_out_r2_paired", | 233 "output_name": "fastq_out_r2_paired", |
| 210 "uuid": "1b2d0dd4-d1ce-4886-b300-8df03d3918fa" | 234 "uuid": "ada191c5-9f20-4052-aa5e-03f73f9587ad" |
| 211 } | 235 } |
| 212 ] | 236 ] |
| 213 }, | 237 }, |
| 214 "5": { | 238 "5": { |
| 215 "annotation": "", | 239 "annotation": "", |
| 240 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
| 241 "id": 5, | |
| 242 "input_connections": { | |
| 243 "input_type|fastq_input1": { | |
| 244 "id": 4, | |
| 245 "output_name": "fastq_out_r1_paired" | |
| 246 }, | |
| 247 "input_type|fastq_input2": { | |
| 248 "id": 4, | |
| 249 "output_name": "fastq_out_r2_paired" | |
| 250 }, | |
| 251 "reference_source|ref_file": { | |
| 252 "id": 2, | |
| 253 "output_name": "output" | |
| 254 } | |
| 255 }, | |
| 256 "inputs": [ | |
| 257 { | |
| 258 "description": "runtime parameter for tool Map with BWA", | |
| 259 "name": "input_type" | |
| 260 }, | |
| 261 { | |
| 262 "description": "runtime parameter for tool Map with BWA", | |
| 263 "name": "input_type" | |
| 264 }, | |
| 265 { | |
| 266 "description": "runtime parameter for tool Map with BWA", | |
| 267 "name": "reference_source" | |
| 268 } | |
| 269 ], | |
| 270 "label": null, | |
| 271 "name": "Map with BWA", | |
| 272 "outputs": [ | |
| 273 { | |
| 274 "name": "bam_output", | |
| 275 "type": "bam" | |
| 276 } | |
| 277 ], | |
| 278 "position": { | |
| 279 "left": 772.5, | |
| 280 "top": 306 | |
| 281 }, | |
| 282 "post_job_actions": {}, | |
| 283 "tool_errors": null, | |
| 284 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
| 285 "tool_shed_repository": { | |
| 286 "changeset_revision": "546ada4a9f43", | |
| 287 "name": "bwa", | |
| 288 "owner": "devteam", | |
| 289 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 290 }, | |
| 291 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"adv_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"input_type_selector\\\": \\\"paired\\\", \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", | |
| 292 "tool_version": "0.7.12.1", | |
| 293 "type": "tool", | |
| 294 "uuid": "3c509fb7-aef9-4e6d-bbb7-f6099d71f15e", | |
| 295 "workflow_outputs": [ | |
| 296 { | |
| 297 "label": null, | |
| 298 "output_name": "bam_output", | |
| 299 "uuid": "d7011177-89c7-48ac-928e-935c6eecf92d" | |
| 300 } | |
| 301 ] | |
| 302 }, | |
| 303 "6": { | |
| 304 "annotation": "", | |
| 305 "content_id": "toolshed.g2.bx.psu.edu/repos/brenninc/samtools_flag_filter_1_2/samtools_flag_filter/0.1", | |
| 306 "id": 6, | |
| 307 "input_connections": { | |
| 308 "input": { | |
| 309 "id": 5, | |
| 310 "output_name": "bam_output" | |
| 311 } | |
| 312 }, | |
| 313 "inputs": [ | |
| 314 { | |
| 315 "description": "runtime parameter for tool Samtools flag_filter", | |
| 316 "name": "input" | |
| 317 } | |
| 318 ], | |
| 319 "label": null, | |
| 320 "name": "Samtools flag_filter", | |
| 321 "outputs": [ | |
| 322 { | |
| 323 "name": "output", | |
| 324 "type": "bam" | |
| 325 } | |
| 326 ], | |
| 327 "position": { | |
| 328 "left": 1004.5, | |
| 329 "top": 303 | |
| 330 }, | |
| 331 "post_job_actions": {}, | |
| 332 "tool_errors": null, | |
| 333 "tool_id": "toolshed.g2.bx.psu.edu/repos/brenninc/samtools_flag_filter_1_2/samtools_flag_filter/0.1", | |
| 334 "tool_shed_repository": { | |
| 335 "changeset_revision": "97bb72be07f9", | |
| 336 "name": "samtools_flag_filter_1_2", | |
| 337 "owner": "brenninc", | |
| 338 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 339 }, | |
| 340 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"bits\": \"[{\\\"__index__\\\": 0, \\\"flag\\\": \\\"0x0004\\\", \\\"state\\\": \\\"f\\\"}]\", \"__page__\": 0}", | |
| 341 "tool_version": "0.1", | |
| 342 "type": "tool", | |
| 343 "uuid": "e31b4dcc-9623-4c50-8139-214e40fe29d0", | |
| 344 "workflow_outputs": [ | |
| 345 { | |
| 346 "label": null, | |
| 347 "output_name": "output", | |
| 348 "uuid": "c9c36760-d2a9-4c05-808c-05a092260670" | |
| 349 } | |
| 350 ] | |
| 351 }, | |
| 352 "7": { | |
| 353 "annotation": "", | |
| 354 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
| 355 "id": 7, | |
| 356 "input_connections": { | |
| 357 "input_type|bam_input": { | |
| 358 "id": 6, | |
| 359 "output_name": "output" | |
| 360 }, | |
| 361 "reference_source|ref_file": { | |
| 362 "id": 3, | |
| 363 "output_name": "output" | |
| 364 } | |
| 365 }, | |
| 366 "inputs": [ | |
| 367 { | |
| 368 "description": "runtime parameter for tool Map with BWA", | |
| 369 "name": "input_type" | |
| 370 }, | |
| 371 { | |
| 372 "description": "runtime parameter for tool Map with BWA", | |
| 373 "name": "reference_source" | |
| 374 } | |
| 375 ], | |
| 376 "label": null, | |
| 377 "name": "Map with BWA", | |
| 378 "outputs": [ | |
| 379 { | |
| 380 "name": "bam_output", | |
| 381 "type": "bam" | |
| 382 } | |
| 383 ], | |
| 384 "position": { | |
| 385 "left": 1279.5, | |
| 386 "top": 305 | |
| 387 }, | |
| 388 "post_job_actions": {}, | |
| 389 "tool_errors": null, | |
| 390 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
| 391 "tool_shed_repository": { | |
| 392 "changeset_revision": "546ada4a9f43", | |
| 393 "name": "bwa", | |
| 394 "owner": "devteam", | |
| 395 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 396 }, | |
| 397 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"bam_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 3, \\\"input_type_selector\\\": \\\"paired_bam\\\", \\\"adv_bam_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", | |
| 398 "tool_version": "0.7.12.1", | |
| 399 "type": "tool", | |
| 400 "uuid": "4dff04dd-4331-4390-a21d-64140a177ce4", | |
| 401 "workflow_outputs": [ | |
| 402 { | |
| 403 "label": null, | |
| 404 "output_name": "bam_output", | |
| 405 "uuid": "341955c7-7ae9-4872-a52a-f6b2f298cba1" | |
| 406 } | |
| 407 ] | |
| 408 }, | |
| 409 "8": { | |
| 410 "annotation": "", | |
| 411 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0", | |
| 412 "id": 8, | |
| 413 "input_connections": { | |
| 414 "input1": { | |
| 415 "id": 7, | |
| 416 "output_name": "bam_output" | |
| 417 } | |
| 418 }, | |
| 419 "inputs": [ | |
| 420 { | |
| 421 "description": "runtime parameter for tool Sort", | |
| 422 "name": "input1" | |
| 423 } | |
| 424 ], | |
| 425 "label": null, | |
| 426 "name": "Sort", | |
| 427 "outputs": [ | |
| 428 { | |
| 429 "name": "output1", | |
| 430 "type": "bam" | |
| 431 } | |
| 432 ], | |
| 433 "position": { | |
| 434 "left": 1506, | |
| 435 "top": 306 | |
| 436 }, | |
| 437 "post_job_actions": {}, | |
| 438 "tool_errors": null, | |
| 439 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0", | |
| 440 "tool_shed_repository": { | |
| 441 "changeset_revision": "a430da4f04cd", | |
| 442 "name": "samtools_sort", | |
| 443 "owner": "devteam", | |
| 444 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 445 }, | |
| 446 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"sort_mode\": \"\\\"-n\\\"\"}", | |
| 447 "tool_version": "2.0", | |
| 448 "type": "tool", | |
| 449 "uuid": "97ca7254-d03b-4cf3-810c-7dbaa6f65e72", | |
| 450 "workflow_outputs": [ | |
| 451 { | |
| 452 "label": null, | |
| 453 "output_name": "output1", | |
| 454 "uuid": "7b4416a5-ff90-4d1a-83c3-24c44e77f640" | |
| 455 } | |
| 456 ] | |
| 457 }, | |
| 458 "9": { | |
| 459 "annotation": "", | |
| 460 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0", | |
| 461 "id": 9, | |
| 462 "input_connections": { | |
| 463 "input1": { | |
| 464 "id": 8, | |
| 465 "output_name": "output1" | |
| 466 } | |
| 467 }, | |
| 468 "inputs": [ | |
| 469 { | |
| 470 "description": "runtime parameter for tool BAM-to-SAM", | |
| 471 "name": "input1" | |
| 472 } | |
| 473 ], | |
| 474 "label": null, | |
| 475 "name": "BAM-to-SAM", | |
| 476 "outputs": [ | |
| 477 { | |
| 478 "name": "output1", | |
| 479 "type": "sam" | |
| 480 } | |
| 481 ], | |
| 482 "position": { | |
| 483 "left": 1507.5, | |
| 484 "top": 433 | |
| 485 }, | |
| 486 "post_job_actions": {}, | |
| 487 "tool_errors": null, | |
| 488 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0", | |
| 489 "tool_shed_repository": { | |
| 490 "changeset_revision": "af7c50162f0b", | |
| 491 "name": "bam_to_sam", | |
| 492 "owner": "devteam", | |
| 493 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 494 }, | |
| 495 "tool_state": "{\"header\": \"\\\"-h\\\"\", \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0}", | |
| 496 "tool_version": "2.0", | |
| 497 "type": "tool", | |
| 498 "uuid": "5196c387-3fad-46dc-9e6f-63af7ffae562", | |
| 499 "workflow_outputs": [ | |
| 500 { | |
| 501 "label": null, | |
| 502 "output_name": "output1", | |
| 503 "uuid": "a4536845-4aaa-4a65-bc1b-e235f762a742" | |
| 504 } | |
| 505 ] | |
| 506 }, | |
| 507 "10": { | |
| 508 "annotation": "", | |
| 216 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", | 509 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", |
| 217 "id": 5, | 510 "id": 10, |
| 218 "input_connections": { | 511 "input_connections": { |
| 219 "input1": { | 512 "input1": { |
| 220 "id": 3, | 513 "id": 3, |
| 221 "output_name": "output" | 514 "output_name": "output" |
| 515 }, | |
| 516 "sam_type|sampe_input2": { | |
| 517 "id": 9, | |
| 518 "output_name": "output1" | |
| 222 } | 519 } |
| 223 }, | 520 }, |
| 224 "inputs": [ | 521 "inputs": [ |
| 225 { | 522 { |
| 226 "description": "runtime parameter for tool Snip Finder", | 523 "description": "runtime parameter for tool Snip Finder", |
| 253 "tool_shed": "toolshed.g2.bx.psu.edu" | 550 "tool_shed": "toolshed.g2.bx.psu.edu" |
| 254 }, | 551 }, |
| 255 "tool_state": "{\"sam_type\": \"{\\\"best\\\": \\\"false\\\", \\\"mode\\\": \\\"paired_end\\\", \\\"__current_case__\\\": 1, \\\"sampe_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", | 552 "tool_state": "{\"sam_type\": \"{\\\"best\\\": \\\"false\\\", \\\"mode\\\": \\\"paired_end\\\", \\\"__current_case__\\\": 1, \\\"sampe_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", |
| 256 "tool_version": "0.1.0", | 553 "tool_version": "0.1.0", |
| 257 "type": "tool", | 554 "type": "tool", |
| 258 "uuid": "e4564c96-a500-4017-a222-fc0e55a23b20", | 555 "uuid": "3c0b1793-8625-4529-a406-6ffa822b38ab", |
| 259 "workflow_outputs": [ | 556 "workflow_outputs": [ |
| 260 { | 557 { |
| 261 "label": null, | 558 "label": null, |
| 262 "output_name": "output1", | 559 "output_name": "output1", |
| 263 "uuid": "44843c44-7cf5-4738-9b48-60ad16b8d915" | 560 "uuid": "b58e3331-4b37-49d9-b311-1120ca9606e6" |
| 264 } | |
| 265 ] | |
| 266 }, | |
| 267 "6": { | |
| 268 "annotation": "", | |
| 269 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
| 270 "id": 6, | |
| 271 "input_connections": { | |
| 272 "input_type|fastq_input1": { | |
| 273 "id": 4, | |
| 274 "output_name": "fastq_out_r1_paired" | |
| 275 }, | |
| 276 "input_type|fastq_input2": { | |
| 277 "id": 4, | |
| 278 "output_name": "fastq_out_r2_paired" | |
| 279 }, | |
| 280 "reference_source|ref_file": { | |
| 281 "id": 2, | |
| 282 "output_name": "output" | |
| 283 } | |
| 284 }, | |
| 285 "inputs": [ | |
| 286 { | |
| 287 "description": "runtime parameter for tool Map with BWA", | |
| 288 "name": "input_type" | |
| 289 }, | |
| 290 { | |
| 291 "description": "runtime parameter for tool Map with BWA", | |
| 292 "name": "input_type" | |
| 293 }, | |
| 294 { | |
| 295 "description": "runtime parameter for tool Map with BWA", | |
| 296 "name": "reference_source" | |
| 297 } | |
| 298 ], | |
| 299 "label": null, | |
| 300 "name": "Map with BWA", | |
| 301 "outputs": [ | |
| 302 { | |
| 303 "name": "bam_output", | |
| 304 "type": "bam" | |
| 305 } | |
| 306 ], | |
| 307 "position": { | |
| 308 "left": 772.5, | |
| 309 "top": 306 | |
| 310 }, | |
| 311 "post_job_actions": {}, | |
| 312 "tool_errors": null, | |
| 313 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
| 314 "tool_shed_repository": { | |
| 315 "changeset_revision": "546ada4a9f43", | |
| 316 "name": "bwa", | |
| 317 "owner": "devteam", | |
| 318 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 319 }, | |
| 320 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"adv_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"input_type_selector\\\": \\\"paired\\\", \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", | |
| 321 "tool_version": "0.7.12.1", | |
| 322 "type": "tool", | |
| 323 "uuid": "880e395c-e063-4ae9-803c-b1961ef0a4fd", | |
| 324 "workflow_outputs": [ | |
| 325 { | |
| 326 "label": null, | |
| 327 "output_name": "bam_output", | |
| 328 "uuid": "8b9ad567-40bb-4533-9342-ca2c7a57326a" | |
| 329 } | |
| 330 ] | |
| 331 }, | |
| 332 "7": { | |
| 333 "annotation": "", | |
| 334 "content_id": "toolshed.g2.bx.psu.edu/repos/brenninc/samtools_flag_filter_1_2/samtools_flag_filter/0.1", | |
| 335 "id": 7, | |
| 336 "input_connections": { | |
| 337 "input": { | |
| 338 "id": 6, | |
| 339 "output_name": "bam_output" | |
| 340 } | |
| 341 }, | |
| 342 "inputs": [ | |
| 343 { | |
| 344 "description": "runtime parameter for tool Samtools flag_filter", | |
| 345 "name": "input" | |
| 346 } | |
| 347 ], | |
| 348 "label": null, | |
| 349 "name": "Samtools flag_filter", | |
| 350 "outputs": [ | |
| 351 { | |
| 352 "name": "output", | |
| 353 "type": "bam" | |
| 354 } | |
| 355 ], | |
| 356 "position": { | |
| 357 "left": 1004.5, | |
| 358 "top": 303 | |
| 359 }, | |
| 360 "post_job_actions": {}, | |
| 361 "tool_errors": null, | |
| 362 "tool_id": "toolshed.g2.bx.psu.edu/repos/brenninc/samtools_flag_filter_1_2/samtools_flag_filter/0.1", | |
| 363 "tool_shed_repository": { | |
| 364 "changeset_revision": "97bb72be07f9", | |
| 365 "name": "samtools_flag_filter_1_2", | |
| 366 "owner": "brenninc", | |
| 367 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 368 }, | |
| 369 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"bits\": \"[{\\\"__index__\\\": 0, \\\"flag\\\": \\\"0x0004\\\", \\\"state\\\": \\\"f\\\"}]\", \"__page__\": 0}", | |
| 370 "tool_version": "0.1", | |
| 371 "type": "tool", | |
| 372 "uuid": "aa177899-8618-4afb-b484-e2a9eb616f04", | |
| 373 "workflow_outputs": [ | |
| 374 { | |
| 375 "label": null, | |
| 376 "output_name": "output", | |
| 377 "uuid": "a960b5e7-cb47-4afb-9688-3a787b4813a5" | |
| 378 } | |
| 379 ] | |
| 380 }, | |
| 381 "8": { | |
| 382 "annotation": "", | |
| 383 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
| 384 "id": 8, | |
| 385 "input_connections": { | |
| 386 "input_type|bam_input": { | |
| 387 "id": 7, | |
| 388 "output_name": "output" | |
| 389 }, | |
| 390 "reference_source|ref_file": { | |
| 391 "id": 3, | |
| 392 "output_name": "output" | |
| 393 } | |
| 394 }, | |
| 395 "inputs": [ | |
| 396 { | |
| 397 "description": "runtime parameter for tool Map with BWA", | |
| 398 "name": "input_type" | |
| 399 }, | |
| 400 { | |
| 401 "description": "runtime parameter for tool Map with BWA", | |
| 402 "name": "reference_source" | |
| 403 } | |
| 404 ], | |
| 405 "label": null, | |
| 406 "name": "Map with BWA", | |
| 407 "outputs": [ | |
| 408 { | |
| 409 "name": "bam_output", | |
| 410 "type": "bam" | |
| 411 } | |
| 412 ], | |
| 413 "position": { | |
| 414 "left": 1279.5, | |
| 415 "top": 305 | |
| 416 }, | |
| 417 "post_job_actions": {}, | |
| 418 "tool_errors": null, | |
| 419 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
| 420 "tool_shed_repository": { | |
| 421 "changeset_revision": "546ada4a9f43", | |
| 422 "name": "bwa", | |
| 423 "owner": "devteam", | |
| 424 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 425 }, | |
| 426 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"bam_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 3, \\\"input_type_selector\\\": \\\"paired_bam\\\", \\\"adv_bam_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", | |
| 427 "tool_version": "0.7.12.1", | |
| 428 "type": "tool", | |
| 429 "uuid": "91a7471e-ee8d-4f6f-8002-d0914dd8df57", | |
| 430 "workflow_outputs": [ | |
| 431 { | |
| 432 "label": null, | |
| 433 "output_name": "bam_output", | |
| 434 "uuid": "70c657a7-61ce-4c52-a5b4-564eddd9e79e" | |
| 435 } | |
| 436 ] | |
| 437 }, | |
| 438 "9": { | |
| 439 "annotation": "", | |
| 440 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0", | |
| 441 "id": 9, | |
| 442 "input_connections": { | |
| 443 "input1": { | |
| 444 "id": 8, | |
| 445 "output_name": "bam_output" | |
| 446 } | |
| 447 }, | |
| 448 "inputs": [ | |
| 449 { | |
| 450 "description": "runtime parameter for tool Sort", | |
| 451 "name": "input1" | |
| 452 } | |
| 453 ], | |
| 454 "label": null, | |
| 455 "name": "Sort", | |
| 456 "outputs": [ | |
| 457 { | |
| 458 "name": "output1", | |
| 459 "type": "bam" | |
| 460 } | |
| 461 ], | |
| 462 "position": { | |
| 463 "left": 1506, | |
| 464 "top": 306 | |
| 465 }, | |
| 466 "post_job_actions": {}, | |
| 467 "tool_errors": null, | |
| 468 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0", | |
| 469 "tool_shed_repository": { | |
| 470 "changeset_revision": "a430da4f04cd", | |
| 471 "name": "samtools_sort", | |
| 472 "owner": "devteam", | |
| 473 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 474 }, | |
| 475 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"sort_mode\": \"\\\"-n\\\"\"}", | |
| 476 "tool_version": "2.0", | |
| 477 "type": "tool", | |
| 478 "uuid": "62d071ac-483d-43d0-a7a2-59cd7c41ee39", | |
| 479 "workflow_outputs": [ | |
| 480 { | |
| 481 "label": null, | |
| 482 "output_name": "output1", | |
| 483 "uuid": "b6efbbfd-4e6b-410c-a99d-f8dd4e600ea9" | |
| 484 } | |
| 485 ] | |
| 486 }, | |
| 487 "10": { | |
| 488 "annotation": "", | |
| 489 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0", | |
| 490 "id": 10, | |
| 491 "input_connections": { | |
| 492 "input1": { | |
| 493 "id": 9, | |
| 494 "output_name": "output1" | |
| 495 } | |
| 496 }, | |
| 497 "inputs": [ | |
| 498 { | |
| 499 "description": "runtime parameter for tool BAM-to-SAM", | |
| 500 "name": "input1" | |
| 501 } | |
| 502 ], | |
| 503 "label": null, | |
| 504 "name": "BAM-to-SAM", | |
| 505 "outputs": [ | |
| 506 { | |
| 507 "name": "output1", | |
| 508 "type": "sam" | |
| 509 } | |
| 510 ], | |
| 511 "position": { | |
| 512 "left": 1507.5, | |
| 513 "top": 433 | |
| 514 }, | |
| 515 "post_job_actions": {}, | |
| 516 "tool_errors": null, | |
| 517 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0", | |
| 518 "tool_shed_repository": { | |
| 519 "changeset_revision": "af7c50162f0b", | |
| 520 "name": "bam_to_sam", | |
| 521 "owner": "devteam", | |
| 522 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 523 }, | |
| 524 "tool_state": "{\"header\": \"\\\"-h\\\"\", \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0}", | |
| 525 "tool_version": "2.0", | |
| 526 "type": "tool", | |
| 527 "uuid": "5076f37b-5da6-44a3-a3b2-f4172d547dc3", | |
| 528 "workflow_outputs": [ | |
| 529 { | |
| 530 "label": null, | |
| 531 "output_name": "output1", | |
| 532 "uuid": "4b52f2d0-1a66-408a-bc99-0da79cc8542f" | |
| 533 } | 561 } |
| 534 ] | 562 ] |
| 535 }, | 563 }, |
| 536 "11": { | 564 "11": { |
| 537 "annotation": "", | 565 "annotation": "", |
| 541 "input1": { | 569 "input1": { |
| 542 "id": 3, | 570 "id": 3, |
| 543 "output_name": "output" | 571 "output_name": "output" |
| 544 }, | 572 }, |
| 545 "input2": { | 573 "input2": { |
| 546 "id": 10, | 574 "id": 9, |
| 547 "output_name": "output1" | 575 "output_name": "output1" |
| 548 } | 576 } |
| 549 }, | 577 }, |
| 550 "inputs": [ | 578 "inputs": [ |
| 551 { | 579 { |
| 585 "tool_shed": "toolshed.g2.bx.psu.edu" | 613 "tool_shed": "toolshed.g2.bx.psu.edu" |
| 586 }, | 614 }, |
| 587 "tool_state": "{\"input2\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min\": \"\\\"5\\\"\", \"max\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"samples\": \"\\\"1\\\"\", \"skip\": \"\\\"5\\\"\", \"threshold\": \"\\\"80\\\"\"}", | 615 "tool_state": "{\"input2\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min\": \"\\\"5\\\"\", \"max\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"samples\": \"\\\"1\\\"\", \"skip\": \"\\\"5\\\"\", \"threshold\": \"\\\"80\\\"\"}", |
| 588 "tool_version": "0.1.0", | 616 "tool_version": "0.1.0", |
| 589 "type": "tool", | 617 "type": "tool", |
| 590 "uuid": "a79d4e7c-dc9c-45fc-bc5f-e07c8289dc6c", | 618 "uuid": "0907193f-3458-40a1-b0ba-beac3998da62", |
| 591 "workflow_outputs": [] | 619 "workflow_outputs": [] |
| 592 } | 620 } |
| 593 }, | 621 }, |
| 594 "uuid": "882a41f1-f16c-4e06-a19b-21a5ffc1fd36" | 622 "uuid": "5f790d55-b08b-45e8-8471-005678ec4eef" |
| 595 } | 623 } |
