Mercurial > repos > eschen42 > mqppep_anova
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 |
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date | Sat, 26 Mar 2022 02:27:12 +0000 |
parents | 6679616d0c18 |
children | 1de24bf8867c |
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14:6679616d0c18 | 15:2c5f1a2fe16a |
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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", |
29 "outputs": [], | 29 "outputs": [], |
30 "position": { | 30 "position": { |
31 "bottom": 346.3999938964844, | 31 "bottom": 336.19168853759766, |
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35 "top": 264.5, | 35 "top": 253.99168395996094, |
36 "width": 200, | 36 "width": 200.00001525878906, |
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38 "y": 264.5 | 38 "y": 253.99168395996094 |
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40 "tool_id": null, | 40 "tool_id": null, |
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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68 "width": 200.00001525878906, | |
69 "x": 510.5917053222656, | |
70 "y": 361.7083435058594 | |
71 }, | |
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73 "tool_state": "{\"default\": \"^Intensity[^_]\", \"parameter_type\": \"text\", \"optional\": true}", | |
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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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101 "x": 526.6583862304688, | |
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103 }, | |
104 "tool_id": null, | |
105 "tool_state": "{\"default\": \"\\\\.\\\\d+[A-Z]$\", \"parameter_type\": \"text\", \"optional\": true}", | |
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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, | |
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137 "tool_state": "{\"default\": \"\\\\d+\", \"parameter_type\": \"text\", \"optional\": true}", | |
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": { | |
159 "bottom": 788.8083648681641, | |
160 "height": 61.80000305175781, | |
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162 "right": 734.5750274658203, | |
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165 "x": 534.5750122070312, | |
166 "y": 727.0083618164062 | |
167 }, | |
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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": [], |
62 "position": { | 190 "position": { |
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67 "top": 606.5, | 195 "top": 882.0083618164062, |
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70 "y": 606.5 | 198 "y": 882.0083618164062 |
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73 "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}", | 201 "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"\"}", |
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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, |
82 "errors": null, | 210 "errors": null, |
83 "id": 2, | 211 "id": 6, |
84 "input_connections": {}, | 212 "input_connections": {}, |
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": { |
95 "bottom": 853.8000030517578, | 223 "bottom": 1115.6083679199219, |
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102 "y": 751.5 | 230 "y": 1013.0083618164062 |
103 }, | 231 }, |
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105 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}", | 233 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}", |
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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": { |
127 "bottom": 977.3999938964844, | 255 "bottom": 1224.2084274291992, |
128 "height": 81.89999389648438, | 256 "height": 82.20000457763672, |
129 "left": 708, | 257 "left": 593.6000366210938, |
130 "right": 908, | 258 "right": 793.6000518798828, |
131 "top": 895.5, | 259 "top": 1142.0084228515625, |
132 "width": 200, | 260 "width": 200.00001525878906, |
133 "x": 708, | 261 "x": 593.6000366210938, |
134 "y": 895.5 | 262 "y": 1142.0084228515625 |
135 }, | 263 }, |
136 "tool_id": null, | 264 "tool_id": null, |
137 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}", | 265 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}", |
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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": { |
159 "bottom": 1126.8000030517578, | 287 "bottom": 1354.6084289550781, |
160 "height": 102.30000305175781, | 288 "height": 102.60000610351562, |
161 "left": 729, | 289 "left": 593.5916748046875, |
162 "right": 929, | 290 "right": 793.5916900634766, |
163 "top": 1024.5, | 291 "top": 1252.0084228515625, |
164 "width": 200, | 292 "width": 200.00001525878906, |
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166 "y": 1024.5 | 294 "y": 1252.0084228515625 |
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168 "tool_id": null, | 296 "tool_id": null, |
169 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}", | 297 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}", |
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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197 "x": 745, | 325 "x": 594.5916748046875, |
198 "y": 1169.5 | 326 "y": 1382.0084228515625 |
199 }, | 327 }, |
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201 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}", | 329 "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}", |
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": [], |
222 "position": { | 350 "position": { |
223 "bottom": 1501.8999938964844, | 351 "bottom": 1723.7084274291992, |
224 "height": 81.89999389648438, | 352 "height": 82.20000457763672, |
225 "left": 727, | 353 "left": 611.558349609375, |
226 "right": 927, | 354 "right": 811.5583648681641, |
227 "top": 1420, | 355 "top": 1641.5084228515625, |
228 "width": 200, | 356 "width": 200.00001525878906, |
229 "x": 727, | 357 "x": 611.558349609375, |
230 "y": 1420 | 358 "y": 1641.5084228515625 |
231 }, | 359 }, |
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": { |
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433 | |
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673 "label": "intensities_randomly-imputed_report", | 820 "label": "intensities_randomly-imputed_report", |
674 "output_name": "report_file", | 821 "output_name": "report_file", |
675 "uuid": "d6701a61-357b-4a27-8154-ca41eb16d8a6" | 822 "uuid": "2c54a01e-ca12-4769-b370-cf137fe4b3f4" |
676 }, | 823 }, |
677 { | 824 { |
678 "label": "intensities_randomly-imputed_QN_LT", | 825 "label": "intensities_randomly-imputed_QN_LT", |
679 "output_name": "imp_qn_lt_file", | 826 "output_name": "imp_qn_lt_file", |
680 "uuid": "637faf12-0d52-45b3-a318-40bfc7fcd4cb" | 827 "uuid": "5fa4acc2-b82f-41e8-aedc-6efdc73f3d58" |
681 } | 828 } |
682 ] | 829 ] |
683 } | 830 } |
684 }, | 831 }, |
685 "tags": [ | 832 "tags": [ |
686 "ppenrich" | 833 "ppenrich" |
687 ], | 834 ], |
688 "uuid": "445a0eb0-25c7-44c0-8259-a3346b01cbf3", | 835 "uuid": "23c8a0f0-218f-4ba7-9470-ec826d16243a", |
689 "version": 3 | 836 "version": 19 |
690 } | 837 } |