Mercurial > repos > eschen42 > mqppep_anova

comparison workflow/ppenrich_suite_wf.ga @ 14:6679616d0c18 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 514e7b9b3a3730a5676821554449d5feb323eb9a"
author eschen42
date Tue, 22 Mar 2022 23:12:18 +0000
parents b41a077af3aa
children 2c5f1a2fe16a
comparison
equal deleted inserted replaced
13:b41a077af3aa 14:6679616d0c18
426 "action_type": "RenameDatasetAction", 426 "action_type": "RenameDatasetAction",
427 "output_name": "quantData_tabular" 427 "output_name": "quantData_tabular"
428 } 428 }
429 }, 429 },
430 "tool_id": "mqppep_preproc", 430 "tool_id": "mqppep_preproc",
431 "tool_state": "{\"collapseFunc\": \"sum\", \"intervalCol\": \"1\", \"localProbCutoff\": \"0.75\", \"merge_function\": \"sum\", \"networkin\": {\"__class__\": \"ConnectedValue\"}, \"p_sty_motifs\": {\"__class__\": \"ConnectedValue\"}, \"phosphoCol\": \"^Number of Phospho [(]STY[)]$\", \"phosphoSites\": {\"__class__\": \"ConnectedValue\"}, \"protein_fasta\": {\"__class__\": \"ConnectedValue\"}, \"psp_kinase_substrate\": {\"__class__\": \"ConnectedValue\"}, \"psp_regulatory_sites\": {\"__class__\": \"ConnectedValue\"}, \"pst_not_py\": \"true\", \"species\": \"human\", \"startCol\": \"^Intensity[^_]\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", 431
432
433
434
435
436
437 "tool_state": "{\"collapseFunc\": \"sum\", \"intervalCol\": \"1\", \"localProbCutoff\": \"0.75\", \"merge_function\": \"sum\", \"networkin\": {\"__class__\": \"ConnectedValue\"}, \"p_sty_motifs\": {\"__class__\": \"ConnectedValue\"}, \"phosphoCol\": \"^Number of Phospho [(]STY[)]$\", \"phosphoSites\": {\"__class__\": \"ConnectedValue\"}, \"protein_fasta\": {\"__class__\": \"ConnectedValue\"}, \"psp_kinase_substrate\": {\"__class__\": \"ConnectedValue\"}, \"psp_regulatory_sites\": {\"__class__\": \"ConnectedValue\"}, \"pst_not_py\": \"true\", \"pst_py_selector\": \"st\", \"species\": \"human\", \"startCol\": \"^Intensity[^_]\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
432 "tool_version": null, 438 "tool_version": null,
433 "type": "tool", 439 "type": "tool",
434 "uuid": "1e983dba-edca-4aed-a589-49b1651b4a85", 440 "uuid": "1e983dba-edca-4aed-a589-49b1651b4a85",
435 "workflow_outputs": [ 441 "workflow_outputs": [
436 { 442 {
519 "label": "MaxQuant Phosphopeptide ANOVA group-median imputed", 525 "label": "MaxQuant Phosphopeptide ANOVA group-median imputed",
520 "name": "MaxQuant Phosphopeptide ANOVA", 526 "name": "MaxQuant Phosphopeptide ANOVA",
521 "outputs": [ 527 "outputs": [
522 { 528 {
523 "name": "imputed_data_file", 529 "name": "imputed_data_file",
530 "type": "tabular"
531 },
532 {
533 "name": "imp_qn_lt_file",
524 "type": "tabular" 534 "type": "tabular"
525 }, 535 },
526 { 536 {
527 "name": "report_file", 537 "name": "report_file",
528 "type": "pdf" 538 "type": "pdf"
542 "RenameDatasetActionimputed_data_file": { 552 "RenameDatasetActionimputed_data_file": {
543 "action_arguments": { 553 "action_arguments": {
544 "newname": "#{input_file}.intensities_group-mean-imputed_QN_LT" 554 "newname": "#{input_file}.intensities_group-mean-imputed_QN_LT"
545 }, 555 },
546 "action_type": "RenameDatasetAction", 556 "action_type": "RenameDatasetAction",
557 "output_name": "imp_qn_lt_file"
558 },
559 "RenameDatasetActionimputed_data_file": {
560 "action_arguments": {
561 "newname": "#{input_file}.intensities_group-mean-imputed"
562 },
563 "action_type": "RenameDatasetAction",
547 "output_name": "imputed_data_file" 564 "output_name": "imputed_data_file"
548 }, 565 },
549 "RenameDatasetActionreport_file": { 566 "RenameDatasetActionreport_file": {
550 "action_arguments": { 567 "action_arguments": {
551 "newname": "#{input_file}.intensities_group-mean-imputed_report (download/unzip to view)" 568 "newname": "#{input_file}.intensities_group-mean-imputed_report (download/unzip to view)"
560 "type": "tool", 577 "type": "tool",
561 "uuid": "ffa771c3-c52d-42a4-b78f-a60a39678792", 578 "uuid": "ffa771c3-c52d-42a4-b78f-a60a39678792",
562 "workflow_outputs": [ 579 "workflow_outputs": [
563 { 580 {
564 "label": "intensities_group-mean-imputed_QN_LT", 581 "label": "intensities_group-mean-imputed_QN_LT",
582 "output_name": "imp_qn_lt_file",
583 "uuid": "0e77a2e0-bd7a-4487-aaa6-ead2469509a2"
584 },
585 {
586 "label": "intensities_group-mean-imputed",
565 "output_name": "imputed_data_file", 587 "output_name": "imputed_data_file",
566 "uuid": "169d677f-0acb-4c56-b057-21f4aaf2b920" 588 "uuid": "169d677f-0acb-4c56-b057-21f4aaf2b920"
567 }, 589 },
568 { 590 {
569 "label": "intensities_group-mean-imputed_report", 591 "label": "intensities_group-mean-imputed_report",
591 "label": "MaxQuant Phosphopeptide ANOVA randomly imputed", 613 "label": "MaxQuant Phosphopeptide ANOVA randomly imputed",
592 "name": "MaxQuant Phosphopeptide ANOVA", 614 "name": "MaxQuant Phosphopeptide ANOVA",
593 "outputs": [ 615 "outputs": [
594 { 616 {
595 "name": "imputed_data_file", 617 "name": "imputed_data_file",
618 "type": "tabular"
619 },
620 {
621 "name": "imp_qn_lt_file",
596 "type": "tabular" 622 "type": "tabular"
597 }, 623 },
598 { 624 {
599 "name": "report_file", 625 "name": "report_file",
600 "type": "pdf" 626 "type": "pdf"
614 "RenameDatasetActionimputed_data_file": { 640 "RenameDatasetActionimputed_data_file": {
615 "action_arguments": { 641 "action_arguments": {
616 "newname": "#{input_file}.intensities_randomly-imputed_QN_LT" 642 "newname": "#{input_file}.intensities_randomly-imputed_QN_LT"
617 }, 643 },
618 "action_type": "RenameDatasetAction", 644 "action_type": "RenameDatasetAction",
645 "output_name": "imp_qn_lt_file"
646 },
647 "RenameDatasetActionimputed_data_file": {
648 "action_arguments": {
649 "newname": "#{input_file}.intensities_randomly-imputed"
650 },
651 "action_type": "RenameDatasetAction",
619 "output_name": "imputed_data_file" 652 "output_name": "imputed_data_file"
620 }, 653 },
621 "RenameDatasetActionreport_file": { 654 "RenameDatasetActionreport_file": {
622 "action_arguments": { 655 "action_arguments": {
623 "newname": "#{input_file}.intensities_randomly-imputed_report (download/unzip to view)" 656 "newname": "#{input_file}.intensities_randomly-imputed_report (download/unzip to view)"
638 }, 671 },
639 { 672 {
640 "label": "intensities_randomly-imputed_report", 673 "label": "intensities_randomly-imputed_report",
641 "output_name": "report_file", 674 "output_name": "report_file",
642 "uuid": "d6701a61-357b-4a27-8154-ca41eb16d8a6" 675 "uuid": "d6701a61-357b-4a27-8154-ca41eb16d8a6"
676 },
677 {
678 "label": "intensities_randomly-imputed_QN_LT",
679 "output_name": "imp_qn_lt_file",
680 "uuid": "637faf12-0d52-45b3-a318-40bfc7fcd4cb"
643 } 681 }
644 ] 682 ]
645 } 683 }
646 }, 684 },
647 "tags": [ 685 "tags": [