comparison workflow/ppenrich_suite_wf.ga @ 15:2c5f1a2fe16a draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
author eschen42
date Sat, 26 Mar 2022 02:27:12 +0000
parents 6679616d0c18
children 1de24bf8867c
comparison
equal deleted inserted replaced
14:6679616d0c18 15:2c5f1a2fe16a
26 ], 26 ],
27 "label": "Phospho (STY)Sites.txt", 27 "label": "Phospho (STY)Sites.txt",
28 "name": "Input dataset", 28 "name": "Input dataset",
29 "outputs": [], 29 "outputs": [],
30 "position": { 30 "position": {
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37 "x": 495, 37 "x": 482.5333557128906,
38 "y": 264.5 38 "y": 253.99168395996094
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41 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}", 41 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}",
42 "tool_version": null, 42 "tool_version": null,
43 "type": "data_input", 43 "type": "data_input",
44 "uuid": "21c3c29d-9e8c-4ece-b585-9e68fed7a93f", 44 "uuid": "78170155-4d6c-461b-a289-bcf0196b87db",
45 "workflow_outputs": [] 45 "workflow_outputs": []
46 }, 46 },
47 "1": { 47 "1": {
48 "annotation": "Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)",
49 "content_id": null,
50 "errors": null,
51 "id": 1,
52 "input_connections": {},
53 "inputs": [
54 {
55 "description": "Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)",
56 "name": "Intensity-column pattern"
57 }
58 ],
59 "label": "Intensity-column pattern",
60 "name": "Input parameter",
61 "outputs": [],
62 "position": {
63 "bottom": 443.9083480834961,
64 "height": 82.20000457763672,
65 "left": 510.5917053222656,
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73 "tool_state": "{\"default\": \"^Intensity[^_]\", \"parameter_type\": \"text\", \"optional\": true}",
74 "tool_version": null,
75 "type": "parameter_input",
76 "uuid": "b1a27840-417c-4e81-9fc3-7d3e3dee6753",
77 "workflow_outputs": []
78 },
79 "2": {
80 "annotation": "Pattern extracting sample-names from names of columns that have peptide intensity data (PERL-compatible regular expression)",
81 "content_id": null,
82 "errors": null,
83 "id": 2,
84 "input_connections": {},
85 "inputs": [
86 {
87 "description": "Pattern extracting sample-names from names of columns that have peptide intensity data (PERL-compatible regular expression)",
88 "name": "Sample-extraction pattern"
89 }
90 ],
91 "label": "Sample-extraction pattern",
92 "name": "Input parameter",
93 "outputs": [],
94 "position": {
95 "bottom": 555.9083480834961,
96 "height": 82.20000457763672,
97 "left": 526.6583862304688,
98 "right": 726.6584014892578,
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104 "tool_id": null,
105 "tool_state": "{\"default\": \"\\\\.\\\\d+[A-Z]$\", \"parameter_type\": \"text\", \"optional\": true}",
106 "tool_version": null,
107 "type": "parameter_input",
108 "uuid": "05fe662c-b0a9-4ae7-8232-1b0a09261ac7",
109 "workflow_outputs": []
110 },
111 "3": {
112 "annotation": "Pattern extracting sample-group from the sample-names that are extracted by 'Sample-extraction pattern' (PERL-compatible regular expression)",
113 "content_id": null,
114 "errors": null,
115 "id": 3,
116 "input_connections": {},
117 "inputs": [
118 {
119 "description": "Pattern extracting sample-group from the sample-names that are extracted by 'Sample-extraction pattern' (PERL-compatible regular expression)",
120 "name": "Group-extraction pattern"
121 }
122 ],
123 "label": "Group-extraction pattern",
124 "name": "Input parameter",
125 "outputs": [],
126 "position": {
127 "bottom": 671.9083786010742,
128 "height": 82.20000457763672,
129 "left": 530.7000122070312,
130 "right": 730.7000274658203,
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138 "tool_version": null,
139 "type": "parameter_input",
140 "uuid": "55d4b63b-8863-4ee4-b504-4b436c6e9684",
141 "workflow_outputs": []
142 },
143 "4": {
144 "annotation": "THIS IS pST BY DEFAULT. Change if your data are enriched for pY.",
145 "content_id": null,
146 "errors": null,
147 "id": 4,
148 "input_connections": {},
149 "inputs": [
150 {
151 "description": "THIS IS pST BY DEFAULT. Change if your data are enriched for pY.",
152 "name": "enrichmentType"
153 }
154 ],
155 "label": "enrichmentType",
156 "name": "Input parameter",
157 "outputs": [],
158 "position": {
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160 "height": 61.80000305175781,
161 "left": 534.5750122070312,
162 "right": 734.5750274658203,
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168 "tool_id": null,
169 "tool_state": "{\"restrictions\": [\"pST\", \"pY\"], \"parameter_type\": \"text\", \"optional\": false}",
170 "tool_version": null,
171 "type": "parameter_input",
172 "uuid": "644c2a42-475d-4757-a58b-46d0d86323d3",
173 "workflow_outputs": []
174 },
175 "5": {
48 "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)", 176 "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)",
49 "content_id": null, 177 "content_id": null,
50 "errors": null, 178 "errors": null,
51 "id": 1, 179 "id": 5,
52 "input_connections": {}, 180 "input_connections": {},
53 "inputs": [ 181 "inputs": [
54 { 182 {
55 "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)", 183 "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)",
56 "name": "SwissProt_Human_Canonical_Isoform.fasta" 184 "name": "SwissProt_Human_Canonical_Isoform.fasta"
58 ], 186 ],
59 "label": "SwissProt_Human_Canonical_Isoform.fasta", 187 "label": "SwissProt_Human_Canonical_Isoform.fasta",
60 "name": "Input dataset", 188 "name": "Input dataset",
61 "outputs": [], 189 "outputs": [],
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74 "tool_version": null, 202 "tool_version": null,
75 "type": "data_input", 203 "type": "data_input",
76 "uuid": "5da7317c-4def-48f3-8eac-af95bd18b290", 204 "uuid": "c190d96f-c9ee-413b-ba19-75808b0eff55",
77 "workflow_outputs": [] 205 "workflow_outputs": []
78 }, 206 },
79 "2": { 207 "6": {
80 "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/)", 208 "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/)",
81 "content_id": null, 209 "content_id": null,
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83 "id": 2, 211 "id": 6,
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85 "inputs": [ 213 "inputs": [
86 { 214 {
87 "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/)", 215 "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/)",
88 "name": "NetworKIN_cutoffscore2.0.tabular" 216 "name": "NetworKIN_cutoffscore2.0.tabular"
90 ], 218 ],
91 "label": "NetworKIN_cutoffscore2.0.tabular", 219 "label": "NetworKIN_cutoffscore2.0.tabular",
92 "name": "Input dataset", 220 "name": "Input dataset",
93 "outputs": [], 221 "outputs": [],
94 "position": { 222 "position": {
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103 }, 231 },
104 "tool_id": null, 232 "tool_id": null,
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107 "type": "data_input", 235 "type": "data_input",
108 "uuid": "2edff8de-4379-45e2-b6b9-6ed4706bbf00", 236 "uuid": "d2783d72-6639-4275-8726-6e32b956aaca",
109 "workflow_outputs": [] 237 "workflow_outputs": []
110 }, 238 },
111 "3": { 239 "7": {
112 "annotation": "Derived from http://hprd.org/serine_motifs, http://hprd.org/tyrosine_motifs, and http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx", 240 "annotation": "Derived from http://hprd.org/serine_motifs, http://hprd.org/tyrosine_motifs, and http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx",
113 "content_id": null, 241 "content_id": null,
114 "errors": null, 242 "errors": null,
115 "id": 3, 243 "id": 7,
116 "input_connections": {}, 244 "input_connections": {},
117 "inputs": [ 245 "inputs": [
118 { 246 {
119 "description": "Derived from http://hprd.org/serine_motifs, http://hprd.org/tyrosine_motifs, and http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx", 247 "description": "Derived from http://hprd.org/serine_motifs, http://hprd.org/tyrosine_motifs, and http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx",
120 "name": "pSTY_Motifs.tabular" 248 "name": "pSTY_Motifs.tabular"
122 ], 250 ],
123 "label": "pSTY_Motifs.tabular", 251 "label": "pSTY_Motifs.tabular",
124 "name": "Input dataset", 252 "name": "Input dataset",
125 "outputs": [], 253 "outputs": [],
126 "position": { 254 "position": {
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138 "tool_version": null, 266 "tool_version": null,
139 "type": "data_input", 267 "type": "data_input",
140 "uuid": "86ebaaf2-b050-4eca-a88b-23a4c1af39f5", 268 "uuid": "e8c138eb-fb7d-4b4b-a5cc-25e000f555e1",
141 "workflow_outputs": [] 269 "workflow_outputs": []
142 }, 270 },
143 "4": { 271 "8": {
144 "annotation": "Derived from Kinase_Substrate_Dataset.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)", 272 "annotation": "Derived from Kinase_Substrate_Dataset.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)",
145 "content_id": null, 273 "content_id": null,
146 "errors": null, 274 "errors": null,
147 "id": 4, 275 "id": 8,
148 "input_connections": {}, 276 "input_connections": {},
149 "inputs": [ 277 "inputs": [
150 { 278 {
151 "description": "Derived from Kinase_Substrate_Dataset.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)", 279 "description": "Derived from Kinase_Substrate_Dataset.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)",
152 "name": "PSP_Kinase_Substrate_Dataset.tabular" 280 "name": "PSP_Kinase_Substrate_Dataset.tabular"
154 ], 282 ],
155 "label": "PSP_Kinase_Substrate_Dataset.tabular", 283 "label": "PSP_Kinase_Substrate_Dataset.tabular",
156 "name": "Input dataset", 284 "name": "Input dataset",
157 "outputs": [], 285 "outputs": [],
158 "position": { 286 "position": {
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165 "x": 729, 293 "x": 593.5916748046875,
166 "y": 1024.5 294 "y": 1252.0084228515625
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170 "tool_version": null, 298 "tool_version": null,
171 "type": "data_input", 299 "type": "data_input",
172 "uuid": "92f16705-a19c-4fb9-b278-3ae8e11f09d8", 300 "uuid": "d6aea327-574a-4657-ba6b-13fa973c182a",
173 "workflow_outputs": [] 301 "workflow_outputs": []
174 }, 302 },
175 "5": { 303 "9": {
176 "annotation": "Derived from Regulatory_sites.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)", 304 "annotation": "Derived from Regulatory_sites.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)",
177 "content_id": null, 305 "content_id": null,
178 "errors": null, 306 "errors": null,
179 "id": 5, 307 "id": 9,
180 "input_connections": {}, 308 "input_connections": {},
181 "inputs": [ 309 "inputs": [
182 { 310 {
183 "description": "Derived from Regulatory_sites.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)", 311 "description": "Derived from Regulatory_sites.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)",
184 "name": "PSP_Regulatory_sites.tabular" 312 "name": "PSP_Regulatory_sites.tabular"
186 ], 314 ],
187 "label": "PSP_Regulatory_sites.tabular", 315 "label": "PSP_Regulatory_sites.tabular",
188 "name": "Input dataset", 316 "name": "Input dataset",
189 "outputs": [], 317 "outputs": [],
190 "position": { 318 "position": {
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192 "height": 81.89999389648438, 320 "height": 82.20000457763672,
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200 "tool_id": null, 328 "tool_id": null,
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202 "tool_version": null, 330 "tool_version": null,
203 "type": "data_input", 331 "type": "data_input",
204 "uuid": "5ab49d93-11e4-4e91-b30b-92269b319879", 332 "uuid": "1cda2502-f848-47d0-af07-d9997021b8c4",
205 "workflow_outputs": [] 333 "workflow_outputs": []
206 }, 334 },
207 "6": { 335 "10": {
208 "annotation": "List of alpha cutoff values for significance testing; text file having no header and a single line for each cutoff value.", 336 "annotation": "List of alpha cutoff values for significance testing; text file having no header and a single line for each cutoff value.",
209 "content_id": null, 337 "content_id": null,
210 "errors": null, 338 "errors": null,
211 "id": 6, 339 "id": 10,
212 "input_connections": {}, 340 "input_connections": {},
213 "inputs": [ 341 "inputs": [
214 { 342 {
215 "description": "List of alpha cutoff values for significance testing; text file having no header and a single line for each cutoff value.", 343 "description": "List of alpha cutoff values for significance testing; text file having no header and a single line for each cutoff value.",
216 "name": "alpha_levels.tabular" 344 "name": "alpha_levels.tabular"
218 ], 346 ],
219 "label": "alpha_levels.tabular", 347 "label": "alpha_levels.tabular",
220 "name": "Input dataset", 348 "name": "Input dataset",
221 "outputs": [], 349 "outputs": [],
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232 "tool_id": null, 360 "tool_id": null,
233 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}", 361 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}",
234 "tool_version": null, 362 "tool_version": null,
235 "type": "data_input", 363 "type": "data_input",
236 "uuid": "481c627c-a4ce-45d7-b659-4f54692aafc7", 364 "uuid": "f59256bb-c823-48d6-923e-e54c6d04e155",
237 "workflow_outputs": [] 365 "workflow_outputs": []
238 }, 366 },
239 "7": { 367 "11": {
240 "annotation": "", 368 "annotation": "Transform the output of MaxQuant for phosphoproteome-enriched samples to prepare it for statistical anlaysis.",
241 "content_id": "mqppep_preproc", 369 "content_id": "mqppep_preproc",
242 "errors": null, 370 "errors": null,
243 "id": 7, 371 "id": 11,
244 "input_connections": { 372 "input_connections": {
245 "networkin": { 373 "networkin": {
246 "id": 2, 374 "id": 6,
247 "output_name": "output" 375 "output_name": "output"
248 }, 376 },
249 "p_sty_motifs": { 377 "p_sty_motifs": {
250 "id": 3, 378 "id": 7,
251 "output_name": "output" 379 "output_name": "output"
252 }, 380 },
253 "phosphoSites": { 381 "phosphoSites": {
254 "id": 0, 382 "id": 0,
255 "output_name": "output" 383 "output_name": "output"
256 }, 384 },
257 "protein_fasta": { 385 "protein_fasta": {
386 "id": 5,
387 "output_name": "output"
388 },
389 "psp_kinase_substrate": {
390 "id": 8,
391 "output_name": "output"
392 },
393 "psp_regulatory_sites": {
394 "id": 9,
395 "output_name": "output"
396 },
397 "pst_py_selector": {
398 "id": 4,
399 "output_name": "output"
400 },
401 "startCol": {
258 "id": 1, 402 "id": 1,
259 "output_name": "output" 403 "output_name": "output"
260 },
261 "psp_kinase_substrate": {
262 "id": 4,
263 "output_name": "output"
264 },
265 "psp_regulatory_sites": {
266 "id": 5,
267 "output_name": "output"
268 } 404 }
269 }, 405 },
270 "inputs": [], 406 "inputs": [],
271 "label": null, 407 "label": "Preprocess MaxQuant Phospho (STY)Sites",
272 "name": "MaxQuant Phosphopeptide Preprocessing", 408 "name": "MaxQuant Phosphopeptide Preprocessing",
273 "outputs": [ 409 "outputs": [
274 { 410 {
275 "name": "phosphoPepIntensities", 411 "name": "phosphoPepIntensities",
276 "type": "tabular" 412 "type": "tabular"
323 "name": "preproc_sqlite", 459 "name": "preproc_sqlite",
324 "type": "sqlite" 460 "type": "sqlite"
325 } 461 }
326 ], 462 ],
327 "position": { 463 "position": {
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331 "right": 1338.5, 467 "right": 1457.100112915039,
332 "top": 615.5, 468 "top": 584,
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