annotate TF_ChIP-Seq_analysis_using_MACS2__hg19.ga @ 5:4bf23bc4f4e2 draft

Update workflows and dependencies
author stemcellcommons
date Fri, 22 Jul 2016 00:07:10 -0400
parents d60e070af736
children e6d80da34425
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364 {
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
365 "description": "runtime parameter for tool MACS2 callpeak",
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
366 "name": "input_control_file"
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
367 },
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
368 {
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
369 "description": "runtime parameter for tool MACS2 callpeak",
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
370 "name": "input_treatment_file"
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
371 }
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
372 ],
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
373 "label": null,
2
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stemcellcommons
parents:
diff changeset
374 "name": "MACS2 callpeak",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
375 "outputs": [
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
376 {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
377 "name": "output_tabular",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
378 "type": "tabular"
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
379 },
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
380 {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
381 "name": "output_broadpeaks",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
382 "type": "bed"
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
383 },
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
384 {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
385 "name": "output_gappedpeaks",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
386 "type": "bed"
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
387 },
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
388 {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
389 "name": "output_narrowpeaks",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
390 "type": "bed"
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
391 },
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
392 {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
393 "name": "output_summits",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
394 "type": "bed"
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
395 },
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
396 {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
397 "name": "output_plot",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
398 "type": "pdf"
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
399 },
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
400 {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
401 "name": "output_treat_pileup",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
402 "type": "bedgraph"
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
403 },
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
404 {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
405 "name": "output_control_lambda",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
406 "type": "bedgraph"
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
407 },
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
408 {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
409 "name": "output_extra_files",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
410 "type": "html"
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
411 }
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
412 ],
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
413 "position": {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
414 "left": 1310.5,
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
415 "top": 358.5
d60e070af736 Shorten workflow file name
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parents:
diff changeset
416 },
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
417 "post_job_actions": {},
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
418 "tool_errors": null,
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
419 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0",
5
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
420 "tool_shed_repository": {
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
421 "changeset_revision": "6d4babad010f",
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
422 "name": "macs2",
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
423 "owner": "iuc",
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
424 "tool_shed": "toolshed.g2.bx.psu.edu"
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
425 },
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
426 "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2451960000\\\", \\\"__current_case__\\\": 0}\", \"bampe\": \"\\\"false\\\"\", \"input_control_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"outputs\": \"[\\\"peaks_tabular\\\", \\\"bdg\\\", \\\"pdf\\\"]\", \"cutoff_options\": \"{\\\"cutoff_options_selector\\\": \\\"qvalue\\\", \\\"qvalue\\\": \\\"0.05\\\", \\\"__current_case__\\\": 1}\", \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"off\\\", \\\"__current_case__\\\": 1}\", \"input_treatment_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 0}\", \"band_width\": \"\\\"300\\\"\"}",
2
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
427 "tool_version": "2.1.0.20151222.0",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
428 "type": "tool",
5
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
429 "uuid": "7d522e1b-10c7-41d6-8fee-455133c85089",
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
430 "workflow_outputs": []
2
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
431 },
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
432 "9": {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
433 "annotation": "",
5
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
434 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0",
2
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
435 "id": 9,
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
436 "input_connections": {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
437 "infile_control": {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
438 "id": 8,
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
439 "output_name": "output_control_lambda"
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
440 },
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
441 "infile_treatment": {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
442 "id": 8,
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
443 "output_name": "output_treat_pileup"
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
444 }
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
445 },
5
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
446 "inputs": [
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
447 {
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
448 "description": "runtime parameter for tool MACS2 bdgcmp",
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
449 "name": "infile_control"
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
450 },
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
451 {
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
452 "description": "runtime parameter for tool MACS2 bdgcmp",
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
453 "name": "infile_treatment"
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
454 }
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
455 ],
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
456 "label": null,
2
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
457 "name": "MACS2 bdgcmp",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
458 "outputs": [
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
459 {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
460 "name": "outfile",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
461 "type": "bedgraph"
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
462 }
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
463 ],
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
464 "position": {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
465 "left": 1648,
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
466 "top": 426.5
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
467 },
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
468 "post_job_actions": {},
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
469 "tool_errors": null,
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
470 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0",
5
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
471 "tool_shed_repository": {
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
472 "changeset_revision": "6d4babad010f",
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
473 "name": "macs2",
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
474 "owner": "iuc",
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
475 "tool_shed": "toolshed.g2.bx.psu.edu"
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
476 },
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
477 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
2
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
478 "tool_version": "2.1.0.20151222.0",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
479 "type": "tool",
5
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
480 "uuid": "dcfd9cac-e8a2-4425-a8fc-1e398710d6ca",
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
481 "workflow_outputs": []
2
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
482 },
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
483 "10": {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
484 "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}",
5
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
485 "content_id": "wig_to_bigWig",
2
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
486 "id": 10,
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
487 "input_connections": {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
488 "input1": {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
489 "id": 9,
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
490 "output_name": "outfile"
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
491 }
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
492 },
5
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
493 "inputs": [
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
494 {
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
495 "description": "runtime parameter for tool Wig/BedGraph-to-bigWig",
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
496 "name": "input1"
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
497 }
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
498 ],
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
499 "label": null,
2
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
500 "name": "Wig/BedGraph-to-bigWig",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
501 "outputs": [
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
502 {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
503 "name": "out_file1",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
504 "type": "bigwig"
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
505 }
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
506 ],
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
507 "position": {
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
508 "left": 1853.046875,
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
509 "top": 447.71875
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
510 },
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
511 "post_job_actions": {},
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
512 "tool_errors": null,
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
513 "tool_id": "wig_to_bigWig",
5
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
514 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}",
2
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
515 "tool_version": "1.1.0",
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
516 "type": "tool",
5
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
517 "uuid": "f5cf8c55-03d2-4fc0-b5fa-5f4be859b628",
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
518 "workflow_outputs": []
2
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stemcellcommons
parents:
diff changeset
519 }
5
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
520 },
4bf23bc4f4e2 Update workflows and dependencies
stemcellcommons
parents: 2
diff changeset
521 "uuid": "9d3dbd7d-2fd7-479f-a582-aa2d84a5d443"
2
d60e070af736 Shorten workflow file name
stemcellcommons
parents:
diff changeset
522 }