Mercurial > repos > stemcellcommons > chipseq_workflows
comparison TF_ChIP-Seq_analysis_using_MACS2__mm10.ga @ 7:f9ffbe563402 draft
Update all workflows
author | stemcellcommons |
---|---|
date | Fri, 22 Jul 2016 14:41:07 -0400 |
parents | 4bf23bc4f4e2 |
children |
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6:e6d80da34425 | 7:f9ffbe563402 |
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424 "tool_shed": "toolshed.g2.bx.psu.edu" | 385 "tool_shed": "toolshed.g2.bx.psu.edu" |
425 }, | 386 }, |
426 "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2150570000\\\", \\\"__current_case__\\\": 1}\", \"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\\\"\"}", | 387 "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2150570000\\\", \\\"__current_case__\\\": 1}\", \"bampe\": \"\\\"false\\\"\", \"input_control_file\": \"null\", \"__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\": \"null\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 0}\", \"band_width\": \"\\\"300\\\"\"}", |
427 "tool_version": "2.1.0.20151222.0", | 388 "tool_version": "2.1.0.20151222.0", |
428 "type": "tool", | 389 "type": "tool", |
429 "uuid": "bbcb3034-f9af-4b45-b877-54822312ddac", | 390 "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7", |
430 "workflow_outputs": [] | 391 "workflow_outputs": [] |
431 }, | 392 }, |
432 "9": { | 393 "9": { |
433 "annotation": "", | 394 "annotation": "", |
434 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", | 395 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", |
441 "infile_treatment": { | 402 "infile_treatment": { |
442 "id": 8, | 403 "id": 8, |
443 "output_name": "output_treat_pileup" | 404 "output_name": "output_treat_pileup" |
444 } | 405 } |
445 }, | 406 }, |
446 "inputs": [ | 407 "inputs": [], |
447 { | |
448 "description": "runtime parameter for tool MACS2 bdgcmp", | |
449 "name": "infile_control" | |
450 }, | |
451 { | |
452 "description": "runtime parameter for tool MACS2 bdgcmp", | |
453 "name": "infile_treatment" | |
454 } | |
455 ], | |
456 "label": null, | 408 "label": null, |
457 "name": "MACS2 bdgcmp", | 409 "name": "MACS2 bdgcmp", |
458 "outputs": [ | 410 "outputs": [ |
459 { | 411 { |
460 "name": "outfile", | 412 "name": "outfile", |
472 "changeset_revision": "6d4babad010f", | 424 "changeset_revision": "6d4babad010f", |
473 "name": "macs2", | 425 "name": "macs2", |
474 "owner": "iuc", | 426 "owner": "iuc", |
475 "tool_shed": "toolshed.g2.bx.psu.edu" | 427 "tool_shed": "toolshed.g2.bx.psu.edu" |
476 }, | 428 }, |
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\\\"}\"}", | 429 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"null\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"null\"}", |
478 "tool_version": "2.1.0.20151222.0", | 430 "tool_version": "2.1.0.20151222.0", |
479 "type": "tool", | 431 "type": "tool", |
480 "uuid": "21c64164-b151-4bc4-88c8-3c3a68401a41", | 432 "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", |
481 "workflow_outputs": [] | 433 "workflow_outputs": [] |
482 }, | 434 }, |
483 "10": { | 435 "10": { |
484 "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}", | 436 "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}", |
485 "content_id": "wig_to_bigWig", | 437 "content_id": "wig_to_bigWig", |
488 "input1": { | 440 "input1": { |
489 "id": 9, | 441 "id": 9, |
490 "output_name": "outfile" | 442 "output_name": "outfile" |
491 } | 443 } |
492 }, | 444 }, |
493 "inputs": [ | 445 "inputs": [], |
494 { | |
495 "description": "runtime parameter for tool Wig/BedGraph-to-bigWig", | |
496 "name": "input1" | |
497 } | |
498 ], | |
499 "label": null, | 446 "label": null, |
500 "name": "Wig/BedGraph-to-bigWig", | 447 "name": "Wig/BedGraph-to-bigWig", |
501 "outputs": [ | 448 "outputs": [ |
502 { | 449 { |
503 "name": "out_file1", | 450 "name": "out_file1", |
509 "top": 447.71875 | 456 "top": 447.71875 |
510 }, | 457 }, |
511 "post_job_actions": {}, | 458 "post_job_actions": {}, |
512 "tool_errors": null, | 459 "tool_errors": null, |
513 "tool_id": "wig_to_bigWig", | 460 "tool_id": "wig_to_bigWig", |
514 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", | 461 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", |
515 "tool_version": "1.1.0", | 462 "tool_version": "1.1.0", |
516 "type": "tool", | 463 "type": "tool", |
517 "uuid": "de37a72c-ebc2-4f4f-9e80-70b11d1be79a", | 464 "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", |
518 "workflow_outputs": [] | 465 "workflow_outputs": [] |
519 } | 466 } |
520 }, | 467 }, |
521 "uuid": "3be7b1f8-3931-40c8-8bb1-7fffbe2826d4" | 468 "uuid": "39cc71c7-4bc2-4aae-8d0b-579055f1e196" |
522 } | 469 } |