Mercurial > repos > drosofff > metavisitor_workflows
comparison Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-2.ga @ 1:3d8eb2c065c7 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit a143c96a3168e4135202479cb58e5a2bcdd153b4
author | drosofff |
---|---|
date | Mon, 11 Apr 2016 13:14:14 -0400 |
parents | 4a47903bb4df |
children | 48b020a0d2f7 |
comparison
equal
deleted
inserted
replaced
0:4a47903bb4df | 1:3d8eb2c065c7 |
---|---|
212 "position": { | 212 "position": { |
213 "left": 776.53125, | 213 "left": 776.53125, |
214 "top": 379.59375 | 214 "top": 379.59375 |
215 }, | 215 }, |
216 "post_job_actions": { | 216 "post_job_actions": { |
217 "ChangeDatatypeActionoutput_sam": { | |
218 "action_arguments": { | |
219 "newtype": "tabular" | |
220 }, | |
221 "action_type": "ChangeDatatypeAction", | |
222 "output_name": "output_sam" | |
223 }, | |
217 "DeleteIntermediatesActionoutput_unaligned_reads_l": { | 224 "DeleteIntermediatesActionoutput_unaligned_reads_l": { |
218 "action_arguments": {}, | 225 "action_arguments": {}, |
219 "action_type": "DeleteIntermediatesAction", | 226 "action_type": "DeleteIntermediatesAction", |
220 "output_name": "output_unaligned_reads_l" | 227 "output_name": "output_unaligned_reads_l" |
221 }, | 228 }, |
264 } | 271 } |
265 ] | 272 ] |
266 }, | 273 }, |
267 "4": { | 274 "4": { |
268 "annotation": "", | 275 "annotation": "", |
276 "content_id": "Grouping1", | |
277 "id": 4, | |
278 "input_connections": { | |
279 "input1": { | |
280 "id": 3, | |
281 "output_name": "output_sam" | |
282 } | |
283 }, | |
284 "inputs": [], | |
285 "label": null, | |
286 "name": "Group", | |
287 "outputs": [ | |
288 { | |
289 "name": "out_file1", | |
290 "type": "tabular" | |
291 } | |
292 ], | |
293 "position": { | |
294 "left": 783.5, | |
295 "top": 783 | |
296 }, | |
297 "post_job_actions": { | |
298 "HideDatasetActionout_file1": { | |
299 "action_arguments": {}, | |
300 "action_type": "HideDatasetAction", | |
301 "output_name": "out_file1" | |
302 } | |
303 }, | |
304 "tool_errors": null, | |
305 "tool_id": "Grouping1", | |
306 "tool_state": "{\"operations\": \"[{\\\"opcol\\\": \\\"1\\\", \\\"__index__\\\": 0, \\\"optype\\\": \\\"length\\\", \\\"opround\\\": \\\"no\\\"}]\", \"__page__\": 0, \"input1\": \"null\", \"ignorelines\": \"[\\\"64\\\"]\", \"groupcol\": \"\\\"3\\\"\", \"__rerun_remap_job_id__\": null, \"ignorecase\": \"\\\"False\\\"\"}", | |
307 "tool_version": "2.1.0", | |
308 "type": "tool", | |
309 "uuid": "731a0b2f-10f8-43d5-840b-892333b92d3c", | |
310 "workflow_outputs": [] | |
311 }, | |
312 "5": { | |
313 "annotation": "", | |
269 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0", | 314 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0", |
270 "id": 4, | 315 "id": 5, |
271 "input_connections": { | 316 "input_connections": { |
272 "input": { | 317 "input": { |
273 "id": 3, | 318 "id": 3, |
274 "output_name": "output_aligned_reads_l" | 319 "output_name": "output_aligned_reads_l" |
275 } | 320 } |
300 "output_name": "output", | 345 "output_name": "output", |
301 "uuid": "72347b83-e33d-48e0-950e-4f9ea61d14ea" | 346 "uuid": "72347b83-e33d-48e0-950e-4f9ea61d14ea" |
302 } | 347 } |
303 ] | 348 ] |
304 }, | 349 }, |
305 "5": { | 350 "6": { |
351 "annotation": "", | |
352 "content_id": "sort1", | |
353 "id": 6, | |
354 "input_connections": { | |
355 "input": { | |
356 "id": 4, | |
357 "output_name": "out_file1" | |
358 } | |
359 }, | |
360 "inputs": [], | |
361 "label": null, | |
362 "name": "Sort", | |
363 "outputs": [ | |
364 { | |
365 "name": "out_file1", | |
366 "type": "input" | |
367 } | |
368 ], | |
369 "position": { | |
370 "left": 1018.5, | |
371 "top": 826 | |
372 }, | |
373 "post_job_actions": { | |
374 "RenameDatasetActionout_file1": { | |
375 "action_arguments": { | |
376 "newname": "putative false negatives" | |
377 }, | |
378 "action_type": "RenameDatasetAction", | |
379 "output_name": "out_file1" | |
380 } | |
381 }, | |
382 "tool_errors": null, | |
383 "tool_id": "sort1", | |
384 "tool_state": "{\"__page__\": 0, \"style\": \"\\\"gennum\\\"\", \"column\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"DESC\\\"\", \"input\": \"null\", \"column_set\": \"[]\"}", | |
385 "tool_version": "1.0.3", | |
386 "type": "tool", | |
387 "uuid": "a586f659-f4bd-4968-8b42-7f1afeea1dfb", | |
388 "workflow_outputs": [ | |
389 { | |
390 "label": null, | |
391 "output_name": "out_file1", | |
392 "uuid": "6369f226-0a21-4108-88e5-d5e99aea324b" | |
393 } | |
394 ] | |
395 }, | |
396 "7": { | |
306 "annotation": "", | 397 "annotation": "", |
307 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", | 398 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", |
308 "id": 5, | 399 "id": 7, |
309 "input_connections": { | 400 "input_connections": { |
310 "inputs_0|input": { | 401 "inputs_0|input": { |
311 "id": 4, | 402 "id": 5, |
312 "output_name": "output" | 403 "output_name": "output" |
313 } | 404 } |
314 }, | 405 }, |
315 "inputs": [], | 406 "inputs": [], |
316 "label": null, | 407 "label": null, |
338 "output_name": "transcripts", | 429 "output_name": "transcripts", |
339 "uuid": "f51ee1b3-fcfe-4db4-b341-713c1f7590dd" | 430 "uuid": "f51ee1b3-fcfe-4db4-b341-713c1f7590dd" |
340 } | 431 } |
341 ] | 432 ] |
342 }, | 433 }, |
343 "6": { | 434 "8": { |
344 "annotation": "", | 435 "annotation": "", |
345 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.07", | 436 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.07", |
346 "id": 6, | 437 "id": 8, |
347 "input_connections": { | 438 "input_connections": { |
348 "db_opts|histdb": { | 439 "db_opts|histdb": { |
349 "id": 1, | 440 "id": 1, |
350 "output_name": "output" | 441 "output_name": "output" |
351 }, | 442 }, |
352 "query": { | 443 "query": { |
353 "id": 5, | 444 "id": 7, |
354 "output_name": "transcripts" | 445 "output_name": "transcripts" |
355 } | 446 } |
356 }, | 447 }, |
357 "inputs": [], | 448 "inputs": [], |
358 "label": null, | 449 "label": null, |
380 "output_name": "output1", | 471 "output_name": "output1", |
381 "uuid": "a63b93b5-5870-4e7b-81bc-345ede8af734" | 472 "uuid": "a63b93b5-5870-4e7b-81bc-345ede8af734" |
382 } | 473 } |
383 ] | 474 ] |
384 }, | 475 }, |
385 "7": { | 476 "9": { |
386 "annotation": "", | 477 "annotation": "", |
387 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", | 478 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", |
388 "id": 7, | 479 "id": 9, |
389 "input_connections": { | 480 "input_connections": { |
390 "blast": { | 481 "blast": { |
391 "id": 6, | 482 "id": 8, |
392 "output_name": "output1" | 483 "output_name": "output1" |
393 }, | 484 }, |
394 "sequences": { | 485 "sequences": { |
395 "id": 5, | 486 "id": 7, |
396 "output_name": "transcripts" | 487 "output_name": "transcripts" |
397 } | 488 } |
398 }, | 489 }, |
399 "inputs": [], | 490 "inputs": [], |
400 "label": null, | 491 "label": null, |
450 "output_name": "tabularOutput", | 541 "output_name": "tabularOutput", |
451 "uuid": "beee945b-3fb7-4340-a727-06c3146717bf" | 542 "uuid": "beee945b-3fb7-4340-a727-06c3146717bf" |
452 } | 543 } |
453 ] | 544 ] |
454 }, | 545 }, |
455 "8": { | 546 "10": { |
456 "annotation": "", | 547 "annotation": "", |
457 "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", | 548 "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
458 "id": 8, | 549 "id": 10, |
459 "input_connections": { | 550 "input_connections": { |
460 "input": { | 551 "input": { |
461 "id": 7, | 552 "id": 9, |
462 "output_name": "tabularOutput" | 553 "output_name": "tabularOutput" |
463 } | 554 } |
464 }, | 555 }, |
465 "inputs": [], | 556 "inputs": [], |
466 "label": null, | 557 "label": null, |
497 "uuid": "a177238a-37d7-469b-a243-1330acc04024" | 588 "uuid": "a177238a-37d7-469b-a243-1330acc04024" |
498 } | 589 } |
499 ] | 590 ] |
500 } | 591 } |
501 }, | 592 }, |
502 "uuid": "c56c85ae-7cca-44ff-b732-50f75db00d0b" | 593 "uuid": "e478bbdb-f34d-48f4-9cb6-b54be280f669" |
503 } | 594 } |