Mercurial > repos > eschen42 > mqppep_anova
comparison workflow/ppenrich_suite_wf.ga @ 20:1de24bf8867c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 927072b0b837f0ebed0def50eb677581af516140"
author | eschen42 |
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date | Wed, 06 Apr 2022 20:09:36 +0000 |
parents | 2c5f1a2fe16a |
children | 61adb8801b73 |
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19:131cbc7dcc55 | 20:1de24bf8867c |
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26 ], | 26 ], |
27 "label": "Phospho (STY)Sites.txt", | 27 "label": "Phospho (STY)Sites.txt", |
28 "name": "Input dataset", | 28 "name": "Input dataset", |
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50 "errors": null, | |
51 "id": 1, | |
52 "input_connections": {}, | |
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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", | |
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85 "2": { | |
48 "annotation": "Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)", | 86 "annotation": "Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)", |
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53 "inputs": [ | 91 "inputs": [ |
54 { | 92 { |
55 "description": "Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)", | 93 "description": "Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)", |
56 "name": "Intensity-column pattern" | 94 "name": "Intensity-column pattern" |
58 ], | 96 ], |
59 "label": "Intensity-column pattern", | 97 "label": "Intensity-column pattern", |
60 "name": "Input parameter", | 98 "name": "Input parameter", |
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80 "annotation": "Pattern extracting sample-names from names of columns that have peptide intensity data (PERL-compatible regular expression)", | 124 "annotation": "Pattern extracting sample-names from names of columns that have peptide intensity data (PERL-compatible regular expression)", |
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87 "description": "Pattern extracting sample-names from names of columns that have peptide intensity data (PERL-compatible regular expression)", | 131 "description": "Pattern extracting sample-names from names of columns that have peptide intensity data (PERL-compatible regular expression)", |
88 "name": "Sample-extraction pattern" | 132 "name": "Sample-extraction pattern" |
90 ], | 134 ], |
91 "label": "Sample-extraction pattern", | 135 "label": "Sample-extraction pattern", |
92 "name": "Input parameter", | 136 "name": "Input parameter", |
93 "outputs": [], | 137 "outputs": [], |
94 "position": { | 138 "position": { |
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161 "4": { | |
112 "annotation": "Pattern extracting sample-group from the sample-names that are extracted by 'Sample-extraction pattern' (PERL-compatible regular expression)", | 162 "annotation": "Pattern extracting sample-group from the sample-names that are extracted by 'Sample-extraction pattern' (PERL-compatible regular expression)", |
113 "content_id": null, | 163 "content_id": null, |
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115 "id": 3, | 165 "id": 4, |
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117 "inputs": [ | 167 "inputs": [ |
118 { | 168 { |
119 "description": "Pattern extracting sample-group from the sample-names that are extracted by 'Sample-extraction pattern' (PERL-compatible regular expression)", | 169 "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" | 170 "name": "Group-extraction pattern" |
122 ], | 172 ], |
123 "label": "Group-extraction pattern", | 173 "label": "Group-extraction pattern", |
124 "name": "Input parameter", | 174 "name": "Input parameter", |
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126 "position": { | 176 "position": { |
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141 "workflow_outputs": [] | 191 "workflow_outputs": [ |
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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": { | |
159 "bottom": 788.8083648681641, | |
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173 "workflow_outputs": [] | |
174 }, | 198 }, |
175 "5": { | 199 "5": { |
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)", | 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)", |
177 "content_id": null, | 201 "content_id": null, |
178 "errors": null, | 202 "errors": null, |
186 ], | 210 ], |
187 "label": "SwissProt_Human_Canonical_Isoform.fasta", | 211 "label": "SwissProt_Human_Canonical_Isoform.fasta", |
188 "name": "Input dataset", | 212 "name": "Input dataset", |
189 "outputs": [], | 213 "outputs": [], |
190 "position": { | 214 "position": { |
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205 "workflow_outputs": [] | 229 "workflow_outputs": [] |
206 }, | 230 }, |
207 "6": { | 231 "6": { |
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/)", | 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/)", |
209 "content_id": null, | 233 "content_id": null, |
218 ], | 242 ], |
219 "label": "NetworKIN_cutoffscore2.0.tabular", | 243 "label": "NetworKIN_cutoffscore2.0.tabular", |
220 "name": "Input dataset", | 244 "name": "Input dataset", |
221 "outputs": [], | 245 "outputs": [], |
222 "position": { | 246 "position": { |
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232 "tool_id": null, | 256 "tool_id": null, |
233 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}", | 257 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}", |
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237 "workflow_outputs": [] | 261 "workflow_outputs": [] |
238 }, | 262 }, |
239 "7": { | 263 "7": { |
240 "annotation": "Derived from http://hprd.org/serine_motifs, http://hprd.org/tyrosine_motifs, and http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx", | 264 "annotation": "Derived from http://hprd.org/serine_motifs, http://hprd.org/tyrosine_motifs, and http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx", |
241 "content_id": null, | 265 "content_id": null, |
250 ], | 274 ], |
251 "label": "pSTY_Motifs.tabular", | 275 "label": "pSTY_Motifs.tabular", |
252 "name": "Input dataset", | 276 "name": "Input dataset", |
253 "outputs": [], | 277 "outputs": [], |
254 "position": { | 278 "position": { |
255 "bottom": 1224.2084274291992, | 279 "bottom": 1336.2092514038086, |
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258 "right": 793.6000518798828, | 282 "right": 873.1686706542969, |
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264 "tool_id": null, | 288 "tool_id": null, |
265 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}", | 289 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}", |
266 "tool_version": null, | 290 "tool_version": null, |
267 "type": "data_input", | 291 "type": "data_input", |
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269 "workflow_outputs": [] | 293 "workflow_outputs": [] |
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271 "8": { | 295 "8": { |
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.)", | 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.)", |
273 "content_id": null, | 297 "content_id": null, |
282 ], | 306 ], |
283 "label": "PSP_Kinase_Substrate_Dataset.tabular", | 307 "label": "PSP_Kinase_Substrate_Dataset.tabular", |
284 "name": "Input dataset", | 308 "name": "Input dataset", |
285 "outputs": [], | 309 "outputs": [], |
286 "position": { | 310 "position": { |
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297 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}", | 321 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}", |
298 "tool_version": null, | 322 "tool_version": null, |
299 "type": "data_input", | 323 "type": "data_input", |
300 "uuid": "d6aea327-574a-4657-ba6b-13fa973c182a", | 324 "uuid": "ed06b46c-d6b3-4d52-a6e6-fa5211da5a0a", |
301 "workflow_outputs": [] | 325 "workflow_outputs": [] |
302 }, | 326 }, |
303 "9": { | 327 "9": { |
304 "annotation": "Derived from Regulatory_sites.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)", | 328 "annotation": "Derived from Regulatory_sites.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use - see that link for citation.)", |
305 "content_id": null, | 329 "content_id": null, |
314 ], | 338 ], |
315 "label": "PSP_Regulatory_sites.tabular", | 339 "label": "PSP_Regulatory_sites.tabular", |
316 "name": "Input dataset", | 340 "name": "Input dataset", |
317 "outputs": [], | 341 "outputs": [], |
318 "position": { | 342 "position": { |
319 "bottom": 1464.2084274291992, | 343 "bottom": 1576.2092514038086, |
320 "height": 82.20000457763672, | 344 "height": 82.1624984741211, |
321 "left": 594.5916748046875, | 345 "left": 674.1561889648438, |
322 "right": 794.5916900634766, | 346 "right": 874.1530456542969, |
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328 "tool_id": null, | 352 "tool_id": null, |
329 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}", | 353 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}", |
330 "tool_version": null, | 354 "tool_version": null, |
331 "type": "data_input", | 355 "type": "data_input", |
332 "uuid": "1cda2502-f848-47d0-af07-d9997021b8c4", | 356 "uuid": "47cf1ca8-315d-425f-bb32-0946cd866d5f", |
333 "workflow_outputs": [] | 357 "workflow_outputs": [] |
334 }, | 358 }, |
335 "10": { | 359 "10": { |
336 "annotation": "List of alpha cutoff values for significance testing; text file having no header and a single line for each cutoff value.", | 360 "annotation": "List of alpha cutoff values for significance testing; text file having no header and a single line for each cutoff value.", |
337 "content_id": null, | 361 "content_id": null, |
346 ], | 370 ], |
347 "label": "alpha_levels.tabular", | 371 "label": "alpha_levels.tabular", |
348 "name": "Input dataset", | 372 "name": "Input dataset", |
349 "outputs": [], | 373 "outputs": [], |
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368 "annotation": "Transform the output of MaxQuant for phosphoproteome-enriched samples to prepare it for statistical anlaysis.", | 392 "annotation": "Transform the output of MaxQuant for phosphoproteome-enriched samples to prepare it for statistical anlaysis.", |
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406 "inputs": [], | 430 "inputs": [ |
431 { | |
432 "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing", | |
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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" | |
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407 "label": "Preprocess MaxQuant Phospho (STY)Sites", | 456 "label": "Preprocess MaxQuant Phospho (STY)Sites", |
408 "name": "MaxQuant Phosphopeptide Preprocessing", | 457 "name": "MaxQuant Phosphopeptide Preprocessing", |
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410 { | 459 { |
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459 "name": "preproc_sqlite", | 508 "name": "preproc_sqlite", |
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663 "label": "ANOVA group-median imputed", | 721 "label": "ANOVA group-median imputed", |
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