Mercurial > repos > galaxyp > mqppep_preproc

comparison workflow/ppenrich_suite_wf.ga @ 0:8dfd5d2b5903 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
author galaxyp
date Mon, 11 Jul 2022 19:22:54 +0000
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-1:000000000000 0:8dfd5d2b5903
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "phoshpoproteomic enrichment data pre-processing and ANOVA",
4 "creator": [
5 {
6 "class": "Person",
7 "identifier": "0000-0002-2882-0508",
8 "name": "Art Eschenlauer"
9 }
10 ],
11 "format-version": "0.1",
12 "license": "MIT",
13 "name": "ppenrich_suite_wf",
14 "steps": {
15 "0": {
16 "annotation": "The Phospho (STY)Sites.txt file produced by MaxQuant (found in the txt folder).",
17 "content_id": null,
18 "errors": null,
19 "id": 0,
20 "input_connections": {},
21 "inputs": [
22 {
23 "description": "The Phospho (STY)Sites.txt file produced by MaxQuant (found in the txt folder).",
24 "name": "Phospho (STY)Sites.txt"
25 }
26 ],
27 "label": "Phospho (STY)Sites.txt",
28 "name": "Input dataset",
29 "outputs": [],
30 "position": {
31 "bottom": 290.16561126708984,
32 "height": 82.1624984741211,
33 "left": 515.090576171875,
34 "right": 715.0874328613281,
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38 "y": 208.00311279296875
39 },
40 "tool_id": null,
41 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}",
42 "tool_version": null,
43 "type": "data_input",
44 "uuid": "c366566c-2a61-4918-b4ea-c1f565c4f2ca",
45 "workflow_outputs": []
46 },
47 "1": {
48 "annotation": "THIS IS pST BY DEFAULT. Change if your data are enriched for pY.",
49 "content_id": null,
50 "errors": null,
51 "id": 1,
52 "input_connections": {},
53 "inputs": [
54 {
55 "description": "THIS IS pST BY DEFAULT. Change if your data are enriched for pY.",
56 "name": "enrichmentType"
57 }
58 ],
59 "label": "enrichmentType",
60 "name": "Input parameter",
61 "outputs": [],
62 "position": {
63 "bottom": 375.7687225341797,
64 "height": 61.76249694824219,
65 "left": 531.1312255859375,
66 "right": 731.1280822753906,
67 "top": 314.0062255859375,
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69 "x": 531.1312255859375,
70 "y": 314.0062255859375
71 },
72 "tool_id": null,
73 "tool_state": "{\"restrictions\": [\"pST\", \"pY\"], \"parameter_type\": \"text\", \"optional\": false}",
74 "tool_version": null,
75 "type": "parameter_input",
76 "uuid": "5f31b776-9e2b-4f3a-a9e6-886ac2062e15",
77 "workflow_outputs": [
78 {
79 "label": null,
80 "output_name": "output",
81 "uuid": "1ff7eb95-9dd3-4006-ab0b-03e4f84a1aa5"
82 }
83 ]
84 },
85 "2": {
86 "annotation": "Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)",
87 "content_id": null,
88 "errors": null,
89 "id": 2,
90 "input_connections": {},
91 "inputs": [
92 {
93 "description": "Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)",
94 "name": "Intensity-column pattern"
95 }
96 ],
97 "label": "Intensity-column pattern",
98 "name": "Input parameter",
99 "outputs": [],
100 "position": {
101 "bottom": 576.2812118530273,
102 "height": 102.56249237060547,
103 "left": 590.1468505859375,
104 "right": 790.1437072753906,
105 "top": 473.7187194824219,
106 "width": 199.99685668945312,
107 "x": 590.1468505859375,
108 "y": 473.7187194824219
109 },
110 "tool_id": null,
111 "tool_state": "{\"default\": \"^Intensity[^_]\", \"parameter_type\": \"text\", \"optional\": true}",
112 "tool_version": null,
113 "type": "parameter_input",
114 "uuid": "86505e43-20be-40f5-ad66-eeb3527c6a60",
115 "workflow_outputs": [
116 {
117 "label": null,
118 "output_name": "output",
119 "uuid": "ebb65015-b681-4798-9504-c8c948f82fee"
120 }
121 ]
122 },
123 "3": {
124 "annotation": "Pattern extracting sample-names from names of columns that have peptide intensity data (PERL-compatible regular expression)",
125 "content_id": null,
126 "errors": null,
127 "id": 3,
128 "input_connections": {},
129 "inputs": [
130 {
131 "description": "Pattern extracting sample-names from names of columns that have peptide intensity data (PERL-compatible regular expression)",
132 "name": "Sample-extraction pattern"
133 }
134 ],
135 "label": "Sample-extraction pattern",
136 "name": "Input parameter",
137 "outputs": [],
138 "position": {
139 "bottom": 688.256217956543,
140 "height": 102.56249237060547,
141 "left": 606.2249755859375,
142 "right": 806.2218322753906,
143 "top": 585.6937255859375,
144 "width": 199.99685668945312,
145 "x": 606.2249755859375,
146 "y": 585.6937255859375
147 },
148 "tool_id": null,
149 "tool_state": "{\"default\": \"\\\\.\\\\d+[A-Z]$\", \"parameter_type\": \"text\", \"optional\": true}",
150 "tool_version": null,
151 "type": "parameter_input",
152 "uuid": "79f4b36c-dd9b-4d24-a9c8-e0084af50597",
153 "workflow_outputs": [
154 {
155 "label": null,
156 "output_name": "output",
157 "uuid": "3f5f7c91-dc90-4e14-84d9-94db5e49a625"
158 }
159 ]
160 },
161 "4": {
162 "annotation": "Pattern extracting sample-group from the sample-names that are extracted by 'Sample-extraction pattern' (PERL-compatible regular expression)",
163 "content_id": null,
164 "errors": null,
165 "id": 4,
166 "input_connections": {},
167 "inputs": [
168 {
169 "description": "Pattern extracting sample-group from the sample-names that are extracted by 'Sample-extraction pattern' (PERL-compatible regular expression)",
170 "name": "Group-extraction pattern"
171 }
172 ],
173 "label": "Group-extraction pattern",
174 "name": "Input parameter",
175 "outputs": [],
176 "position": {
177 "bottom": 804.2999801635742,
178 "height": 102.56249237060547,
179 "left": 610.2562255859375,
180 "right": 810.2530822753906,
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183 "x": 610.2562255859375,
184 "y": 701.7374877929688
185 },
186 "tool_id": null,
187 "tool_state": "{\"default\": \"\\\\d+\", \"parameter_type\": \"text\", \"optional\": true}",
188 "tool_version": null,
189 "type": "parameter_input",
190 "uuid": "67f4321c-9b08-4dd2-b448-813f6fdb1b6a",
191 "workflow_outputs": [
192 {
193 "label": null,
194 "output_name": "output",
195 "uuid": "4abd7c2f-9614-4b08-8ea1-8c5c19d69b7c"
196 }
197 ]
198 },
199 "5": {
200 "annotation": "FASTA file of all human canonical isoforms, derived from Swiss-Prot (e.g., merge of https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot_varsplic.fasta.gz and https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz)",
201 "content_id": null,
202 "errors": null,
203 "id": 5,
204 "input_connections": {},
205 "inputs": [
206 {
207 "description": "FASTA file of all human canonical isoforms, derived from Swiss-Prot (e.g., merge of https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot_varsplic.fasta.gz and https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz)",
208 "name": "SwissProt_Human_Canonical_Isoform.fasta"
209 }
210 ],
211 "label": "SwissProt_Human_Canonical_Isoform.fasta",
212 "name": "Input dataset",
213 "outputs": [],
214 "position": {
215 "bottom": 1096.5749435424805,
216 "height": 102.56249237060547,
217 "left": 639.121826171875,
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220 "width": 199.99685668945312,
221 "x": 639.121826171875,
222 "y": 994.012451171875
223 },
224 "tool_id": null,
225 "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"\"}",
226 "tool_version": null,
227 "type": "data_input",
228 "uuid": "870d3075-3ebb-4505-99a2-c3d01b51a86b",
229 "workflow_outputs": []
230 },
231 "6": {
232 "annotation": "Derived from https://networkin.info/download/networkin_human_predictions_3.1.tsv.xz (which is free for non-commercial use - for required citation, see https://networkin.info/)",
233 "content_id": null,
234 "errors": null,
235 "id": 6,
236 "input_connections": {},
237 "inputs": [
238 {
239 "description": "Derived from https://networkin.info/download/networkin_human_predictions_3.1.tsv.xz (which is free for non-commercial use - for required citation, see https://networkin.info/)",
240 "name": "NetworKIN_cutoffscore2.0.tabular"
241 }
242 ],
243 "label": "NetworKIN_cutoffscore2.0.tabular",
244 "name": "Input dataset",
245 "outputs": [],
246 "position": {
247 "bottom": 1227.581169128418,
248 "height": 102.56249237060547,
249 "left": 656.1561889648438,
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256 "tool_id": null,
257 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}",
258 "tool_version": null,
259 "type": "data_input",
260 "uuid": "0ecd2f07-9b2c-41c5-8bcf-fa45927f61ca",
261 "workflow_outputs": []
262 },
263 "7": {
264 "annotation": "Derived from http://hprd.org/serine_motifs, http://hprd.org/tyrosine_motifs, and http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx",
265 "content_id": null,
266 "errors": null,
267 "id": 7,
268 "input_connections": {},
269 "inputs": [
270 {
271 "description": "Derived from http://hprd.org/serine_motifs, http://hprd.org/tyrosine_motifs, and http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx",
272 "name": "pSTY_Motifs.tabular"
273 }
274 ],
275 "label": "pSTY_Motifs.tabular",
276 "name": "Input dataset",
277 "outputs": [],
278 "position": {
279 "bottom": 1336.2092514038086,
280 "height": 82.1624984741211,
281 "left": 673.1718139648438,
282 "right": 873.1686706542969,
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290 "tool_version": null,
291 "type": "data_input",
292 "uuid": "d8f605d8-4cf6-48dc-9ec5-ceda9f6ee4b2",
293 "workflow_outputs": []
294 },
295 "8": {
296 "annotation": "Derived from Kinase_Substrate_Dataset.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)",
297 "content_id": null,
298 "errors": null,
299 "id": 8,
300 "input_connections": {},
301 "inputs": [
302 {
303 "description": "Derived from Kinase_Substrate_Dataset.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)",
304 "name": "PSP_Kinase_Substrate_Dataset.tabular"
305 }
306 ],
307 "label": "PSP_Kinase_Substrate_Dataset.tabular",
308 "name": "Input dataset",
309 "outputs": [],
310 "position": {
311 "bottom": 1466.596794128418,
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313 "left": 673.1718139648438,
314 "right": 873.1686706542969,
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322 "tool_version": null,
323 "type": "data_input",
324 "uuid": "ed06b46c-d6b3-4d52-a6e6-fa5211da5a0a",
325 "workflow_outputs": []
326 },
327 "9": {
328 "annotation": "Derived from Regulatory_sites.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)",
329 "content_id": null,
330 "errors": null,
331 "id": 9,
332 "input_connections": {},
333 "inputs": [
334 {
335 "description": "Derived from Regulatory_sites.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)",
336 "name": "PSP_Regulatory_sites.tabular"
337 }
338 ],
339 "label": "PSP_Regulatory_sites.tabular",
340 "name": "Input dataset",
341 "outputs": [],
342 "position": {
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345 "left": 674.1561889648438,
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354 "tool_version": null,
355 "type": "data_input",
356 "uuid": "47cf1ca8-315d-425f-bb32-0946cd866d5f",
357 "workflow_outputs": []
358 },
359 "10": {
360 "annotation": "List of alpha cutoff values for significance testing; text file having no header and a single line for each cutoff value.",
361 "content_id": null,
362 "errors": null,
363 "id": 10,
364 "input_connections": {},
365 "inputs": [
366 {
367 "description": "List of alpha cutoff values for significance testing; text file having no header and a single line for each cutoff value.",
368 "name": "alpha_levels.tabular"
369 }
370 ],
371 "label": "alpha_levels.tabular",
372 "name": "Input dataset",
373 "outputs": [],
374 "position": {
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377 "left": 691.1249389648438,
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386 "tool_version": null,
387 "type": "data_input",
388 "uuid": "5d66ff58-9c83-4edd-96c6-6132dc8377c7",
389 "workflow_outputs": []
390 },
391 "11": {
392 "annotation": "Transform the output of MaxQuant for phosphoproteome-enriched samples to prepare it for statistical anlaysis.",
393 "content_id": "mqppep_preproc",
394 "errors": null,
395 "id": 11,
396 "input_connections": {
397 "networkin": {
398 "id": 6,
399 "output_name": "output"
400 },
401 "p_sty_motifs": {
402 "id": 7,
403 "output_name": "output"
404 },
405 "phosphoSites": {
406 "id": 0,
407 "output_name": "output"
408 },
409 "protein_fasta": {
410 "id": 5,
411 "output_name": "output"
412 },
413 "psp_kinase_substrate": {
414 "id": 8,
415 "output_name": "output"
416 },
417 "psp_regulatory_sites": {
418 "id": 9,
419 "output_name": "output"
420 },
421 "pst_py_selector": {
422 "id": 1,
423 "output_name": "output"
424 },
425 "startCol": {
426 "id": 2,
427 "output_name": "output"
428 }
429 },
430 "inputs": [
431 {
432 "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing",
433 "name": "networkin"
434 },
435 {
436 "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing",
437 "name": "p_sty_motifs"
438 },
439 {
440 "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing",
441 "name": "phosphoSites"
442 },
443 {
444 "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing",
445 "name": "protein_fasta"
446 },
447 {
448 "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing",
449 "name": "psp_kinase_substrate"
450 },
451 {
452 "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing",
453 "name": "psp_regulatory_sites"
454 }
455 ],
456 "label": "Preprocess MaxQuant Phospho (STY)Sites",
457 "name": "MaxQuant Phosphopeptide Preprocessing",
458 "outputs": [
459 {
460 "name": "phosphoPepIntensities",
461 "type": "tabular"
462 },
463 {
464 "name": "enrichGraph",
465 "type": "pdf"
466 },
467 {
468 "name": "locProbCutoffGraph",
469 "type": "pdf"
470 },
471 {
472 "name": "enrichGraph_svg",
473 "type": "svg"
474 },
475 {
476 "name": "locProbCutoffGraph_svg",
477 "type": "svg"
478 },
479 {
480 "name": "filteredData_tabular",
481 "type": "tabular"
482 },
483 {
484 "name": "quantData_tabular",
485 "type": "tabular"
486 },
487 {
488 "name": "mapped_phophopeptides",
489 "type": "tabular"
490 },
491 {
492 "name": "melted_phophopeptide_map",
493 "type": "tabular"
494 },
495 {
496 "name": "mqppep_output_sqlite",
497 "type": "sqlite"
498 },
499 {
500 "name": "preproc_tab",
501 "type": "tabular"
502 },
503 {
504 "name": "preproc_csv",
505 "type": "csv"
506 },
507 {
508 "name": "preproc_sqlite",
509 "type": "sqlite"
510 }
511 ],
512 "position": {
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519 "x": 1336.60302734375,
520 "y": 696.0187377929688
521 },
522 "post_job_actions": {
523 "HideDatasetActionfilteredData_tabular": {
524 "action_arguments": {},
525 "action_type": "HideDatasetAction",
526 "output_name": "filteredData_tabular"
527 },
528 "HideDatasetActionmapped_phophopeptides": {
529 "action_arguments": {},
530 "action_type": "HideDatasetAction",
531 "output_name": "mapped_phophopeptides"
532 },
533 "HideDatasetActionmelted_phophopeptide_map": {
534 "action_arguments": {},
535 "action_type": "HideDatasetAction",
536 "output_name": "melted_phophopeptide_map"
537 },
538 "HideDatasetActionmqppep_output_sqlite": {
539 "action_arguments": {},
540 "action_type": "HideDatasetAction",
541 "output_name": "mqppep_output_sqlite"
542 },
543 "HideDatasetActionpreproc_csv": {
544 "action_arguments": {},
545 "action_type": "HideDatasetAction",
546 "output_name": "preproc_csv"
547 },
548 "HideDatasetActionquantData_tabular": {
549 "action_arguments": {},
550 "action_type": "HideDatasetAction",
551 "output_name": "quantData_tabular"
552 },
553 "RenameDatasetActionenrichGraph": {
554 "action_arguments": {
555 "newname": "#{phosphoSites}.enrichGraph_pdf"
556 },
557 "action_type": "RenameDatasetAction",
558 "output_name": "enrichGraph"
559 },
560 "RenameDatasetActionenrichGraph_svg": {
561 "action_arguments": {
562 "newname": "#{phosphoSites}.enrichGraph_svg"
563 },
564 "action_type": "RenameDatasetAction",
565 "output_name": "enrichGraph_svg"
566 },
567 "RenameDatasetActionfilteredData_tabular": {
568 "action_arguments": {
569 "newname": "#{phosphoSites}.filteredData"
570 },
571 "action_type": "RenameDatasetAction",
572 "output_name": "filteredData_tabular"
573 },
574 "RenameDatasetActionlocProbCutoffGraph": {
575 "action_arguments": {
576 "newname": "#{phosphoSites}.locProbCutoffGraph_pdf"
577 },
578 "action_type": "RenameDatasetAction",
579 "output_name": "locProbCutoffGraph"
580 },
581 "RenameDatasetActionlocProbCutoffGraph_svg": {
582 "action_arguments": {
583 "newname": "#{phosphoSites}.locProbCutoffGraph_svg"
584 },
585 "action_type": "RenameDatasetAction",
586 "output_name": "locProbCutoffGraph_svg"
587 },
588 "RenameDatasetActionmapped_phophopeptides": {
589 "action_arguments": {
590 "newname": "#{phosphoSites}.ppep_map"
591 },
592 "action_type": "RenameDatasetAction",
593 "output_name": "mapped_phophopeptides"
594 },
595 "RenameDatasetActionmelted_phophopeptide_map": {
596 "action_arguments": {
597 "newname": "#{phosphoSites}.melted"
598 },
599 "action_type": "RenameDatasetAction",
600 "output_name": "melted_phophopeptide_map"
601 },
602 "RenameDatasetActionmqppep_output_sqlite": {
603 "action_arguments": {
604 "newname": "#{phosphoSites}.ppep_mapping_sqlite"
605 },
606 "action_type": "RenameDatasetAction",
607 "output_name": "mqppep_output_sqlite"
608 },
609 "RenameDatasetActionphosphoPepIntensities": {
610 "action_arguments": {
611 "newname": "#{phosphoSites}.ppep_intensities"
612 },
613 "action_type": "RenameDatasetAction",
614 "output_name": "phosphoPepIntensities"
615 },
616 "RenameDatasetActionpreproc_csv": {
617 "action_arguments": {
618 "newname": "#{phosphoSites}.preproc_csv"
619 },
620 "action_type": "RenameDatasetAction",
621 "output_name": "preproc_csv"
622 },
623 "RenameDatasetActionpreproc_sqlite": {
624 "action_arguments": {
625 "newname": "#{phosphoSites}.preproc_sqlite"
626 },
627 "action_type": "RenameDatasetAction",
628 "output_name": "preproc_sqlite"
629 },
630 "RenameDatasetActionpreproc_tab": {
631 "action_arguments": {
632 "newname": "#{phosphoSites}.preproc_tab"
633 },
634 "action_type": "RenameDatasetAction",
635 "output_name": "preproc_tab"
636 },
637 "RenameDatasetActionquantData_tabular": {
638 "action_arguments": {
639 "newname": "#{phosphoSites}.quantData"
640 },
641 "action_type": "RenameDatasetAction",
642 "output_name": "quantData_tabular"
643 }
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