Mercurial > repos > galaxyp > abrf2017_workshop

comparison Galaxy-Workflow-ABRF_2017_Workflow_for_Functional_Comparison.ga @ 0:eb71034189fb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit bfcee2067ac57cc7136bb6a4281b1748a36776d5
author galaxyp
date Thu, 02 Mar 2017 15:42:24 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:eb71034189fb
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "ABRF 2017 Workflow for Functional Comparison",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "content_id": null,
10 "id": 0,
11 "input_connections": {},
12 "inputs": [
13 {
14 "description": "",
15 "name": "Gene Ontology Terms"
16 }
17 ],
18 "label": null,
19 "name": "Input dataset",
20 "outputs": [],
21 "position": {
22 "left": 177,
23 "top": 188.5
24 },
25 "tool_errors": null,
26 "tool_id": null,
27 "tool_state": "{\"name\": \"Gene Ontology Terms\"}",
28 "tool_version": null,
29 "type": "data_input",
30 "uuid": "6f5a7554-d201-4f17-8e47-8e07ead87e52",
31 "workflow_outputs": [
32 {
33 "label": null,
34 "output_name": "output",
35 "uuid": "1e545169-c1d0-4da0-9f5d-09632dffbd6a"
36 }
37 ]
38 },
39 "1": {
40 "annotation": "",
41 "content_id": null,
42 "id": 1,
43 "input_connections": {},
44 "inputs": [
45 {
46 "description": "",
47 "name": "Bering Strait Pept2Prot (extra fields) Normalized"
48 }
49 ],
50 "label": null,
51 "name": "Input dataset",
52 "outputs": [],
53 "position": {
54 "left": 181,
55 "top": 264.5
56 },
57 "tool_errors": null,
58 "tool_id": null,
59 "tool_state": "{\"name\": \"Bering Strait Pept2Prot (extra fields) Normalized\"}",
60 "tool_version": null,
61 "type": "data_input",
62 "uuid": "caae62e0-46f1-4f84-934f-31be41856bb0",
63 "workflow_outputs": [
64 {
65 "label": null,
66 "output_name": "output",
67 "uuid": "27ccf52d-44c0-43eb-bf66-bee437cfbcfa"
68 }
69 ]
70 },
71 "2": {
72 "annotation": "",
73 "content_id": null,
74 "id": 2,
75 "input_connections": {},
76 "inputs": [
77 {
78 "description": "",
79 "name": "Chukchi Sea Pept2Prot (extra fields) Normalized"
80 }
81 ],
82 "label": null,
83 "name": "Input dataset",
84 "outputs": [],
85 "position": {
86 "left": 185,
87 "top": 354.5
88 },
89 "tool_errors": null,
90 "tool_id": null,
91 "tool_state": "{\"name\": \"Chukchi Sea Pept2Prot (extra fields) Normalized\"}",
92 "tool_version": null,
93 "type": "data_input",
94 "uuid": "3c954f78-1ef3-4cae-bb4e-c768d9904506",
95 "workflow_outputs": [
96 {
97 "label": null,
98 "output_name": "output",
99 "uuid": "67cf7d09-93cf-4e90-9f2c-1f9c61973cff"
100 }
101 ]
102 },
103 "3": {
104 "annotation": "",
105 "content_id": null,
106 "id": 3,
107 "input_connections": {},
108 "inputs": [
109 {
110 "description": "",
111 "name": "Bering Strait PSM Report"
112 }
113 ],
114 "label": null,
115 "name": "Input dataset",
116 "outputs": [],
117 "position": {
118 "left": 187,
119 "top": 442.5
120 },
121 "tool_errors": null,
122 "tool_id": null,
123 "tool_state": "{\"name\": \"Bering Strait PSM Report\"}",
124 "tool_version": null,
125 "type": "data_input",
126 "uuid": "c9826c72-36c9-498e-af09-3ba77ce79885",
127 "workflow_outputs": [
128 {
129 "label": null,
130 "output_name": "output",
131 "uuid": "4c8327ee-cabc-46f6-a3fb-ecf84dca3b8f"
132 }
133 ]
134 },
135 "4": {
136 "annotation": "",
137 "content_id": null,
138 "id": 4,
139 "input_connections": {},
140 "inputs": [
141 {
142 "description": "",
143 "name": "Chukchi Sea PSM Report"
144 }
145 ],
146 "label": null,
147 "name": "Input dataset",
148 "outputs": [],
149 "position": {
150 "left": 190,
151 "top": 523.5
152 },
153 "tool_errors": null,
154 "tool_id": null,
155 "tool_state": "{\"name\": \"Chukchi Sea PSM Report\"}",
156 "tool_version": null,
157 "type": "data_input",
158 "uuid": "6f38f059-5513-4705-b3f0-ff2a3aef638e",
159 "workflow_outputs": [
160 {
161 "label": null,
162 "output_name": "output",
163 "uuid": "2c42d9b6-7107-4354-81dd-40728115bbb1"
164 }
165 ]
166 },
167 "5": {
168 "annotation": "",
169 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0",
170 "id": 5,
171 "input_connections": {
172 "tables_0|table": {
173 "id": 0,
174 "output_name": "output"
175 },
176 "tables_1|table": {
177 "id": 1,
178 "output_name": "output"
179 },
180 "tables_2|table": {
181 "id": 2,
182 "output_name": "output"
183 },
184 "tables_3|table": {
185 "id": 3,
186 "output_name": "output"
187 },
188 "tables_4|table": {
189 "id": 4,
190 "output_name": "output"
191 }
192 },
193 "inputs": [
194 {
195 "description": "runtime parameter for tool Query Tabular",
196 "name": "add_to_database"
197 }
198 ],
199 "label": null,
200 "name": "Query Tabular",
201 "outputs": [
202 {
203 "name": "sqlitedb",
204 "type": "sqlite"
205 },
206 {
207 "name": "output",
208 "type": "tabular"
209 }
210 ],
211 "position": {
212 "left": 440,
213 "top": 230
214 },
215 "post_job_actions": {
216 "RenameDatasetActionoutput": {
217 "action_arguments": {
218 "newname": "BIOLOGICAL PROCESS COMPARISON"
219 },
220 "action_type": "RenameDatasetAction",
221 "output_name": "output"
222 }
223 },
224 "tool_errors": null,
225 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0",
226 "tool_shed_repository": {
227 "changeset_revision": "ae27dab228b8",
228 "name": "query_tabular",
229 "owner": "jjohnson",
230 "tool_shed": "toolshed.g2.bx.psu.edu"
231 },
232 "tool_state": "{\"tables\": \"[{\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"false\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"go\\\", \\\"col_names\\\": \\\"aspect,go_id,description\\\", \\\"indexes\\\": [{\\\"__index__\\\": 0, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"go_id\\\"}, {\\\"__index__\\\": 1, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"aspect,go_id,description\\\"}]}, \\\"__index__\\\": 0, \\\"input_opts\\\": {\\\"linefilters\\\": []}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"false\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"bering\\\", \\\"col_names\\\": \\\"peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_reference,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids\\\", \\\"indexes\\\": [{\\\"__index__\\\": 0, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"go_reference,peptide\\\"}]}, \\\"__index__\\\": 1, \\\"input_opts\\\": {\\\"linefilters\\\": [{\\\"filter\\\": {\\\"comment_char\\\": \\\"#\\\", \\\"__current_case__\\\": 1, \\\"filter_type\\\": \\\"comment\\\"}, \\\"__index__\\\": 0}]}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"false\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"chukchi\\\", \\\"col_names\\\": \\\"peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_reference,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids\\\", \\\"indexes\\\": [{\\\"__index__\\\": 0, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"go_reference,peptide\\\"}]}, \\\"__index__\\\": 2, \\\"input_opts\\\": {\\\"linefilters\\\": [{\\\"filter\\\": {\\\"comment_char\\\": \\\"#\\\", \\\"__current_case__\\\": 1, \\\"filter_type\\\": \\\"comment\\\"}, \\\"__index__\\\": 0}]}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"true\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"bering_psms\\\", \\\"col_names\\\": \\\"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\", \\\"indexes\\\": []}, \\\"__index__\\\": 3, \\\"input_opts\\\": {\\\"linefilters\\\": [{\\\"filter\\\": {\\\"regex_action\\\": \\\"include_match\\\", \\\"regex_pattern\\\": \\\"^\\\\\\\\d\\\", \\\"__current_case__\\\": 2, \\\"filter_type\\\": \\\"regex\\\"}, \\\"__index__\\\": 0}]}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"true\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"chukchi_psms\\\", \\\"col_names\\\": \\\"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\", \\\"indexes\\\": []}, \\\"__index__\\\": 4, \\\"input_opts\\\": {\\\"linefilters\\\": [{\\\"filter\\\": {\\\"regex_action\\\": \\\"include_match\\\", \\\"regex_pattern\\\": \\\"^\\\\\\\\d\\\", \\\"__current_case__\\\": 2, \\\"filter_type\\\": \\\"regex\\\"}, \\\"__index__\\\": 0}]}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\", \"save_db\": \"\\\"true\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\", \"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\",count(distinct c.peptide) as \\\\\\\"chukchi_peptides\\\\\\\",\\\\ncount(distinct b.id)*1.42 as \\\\\\\"bering_psms\\\\\\\", count(distinct c.id) as \\\\\\\"chukchi_psms\\\\\\\"\\\\n FROM go as g LEFT OUTER JOIN\\\\n ( SELECT go.description, bering.peptide, bering_psms.id\\\\n FROM go LEFT OUTER JOIN bering ON go.go_id = bering.go_reference JOIN bering_psms ON bering.peptide = bering_psms.sequence\\\\n GROUP BY go.description, bering.peptide, bering_psms.id\\\\n ) as b ON g.description = b.description LEFT OUTER JOIN\\\\n ( SELECT go.description, chukchi.peptide, chukchi_psms.id\\\\n FROM go LEFT OUTER JOIN chukchi ON go.go_id = chukchi.go_reference JOIN chukchi_psms ON chukchi.peptide = chukchi_psms.sequence\\\\n GROUP BY go.description, chukchi.peptide, chukchi_psms.id\\\\n ) as c ON g.description = c.description\\\\nWHERE g.aspect = 'biological_process'\\\\nGROUP BY g.description\\\\nORDER BY abs(bering_peptides - chukchi_peptides) desc, bering_peptides desc,chukchi_peptides desc\\\"\", \"add_to_database\": \"{\\\"withdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"workdb\": \"\\\"workdb.sqlite\\\"\"}",
233 "tool_version": "2.0.0",
234 "type": "tool",
235 "uuid": "42fb8bde-03c9-4e9d-b003-55d01bb306d6",
236 "workflow_outputs": [
237 {
238 "label": null,
239 "output_name": "output",
240 "uuid": "369c85d5-6d8f-45ca-8f55-01dddce5a4e9"
241 },
242 {
243 "label": null,
244 "output_name": "sqlitedb",
245 "uuid": "fb8dd73d-95c9-48c8-945c-07adf0b13dab"
246 }
247 ]
248 },
249 "6": {
250 "annotation": "",
251 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
252 "id": 6,
253 "input_connections": {
254 "sqlitedb": {
255 "id": 5,
256 "output_name": "sqlitedb"
257 }
258 },
259 "inputs": [
260 {
261 "description": "runtime parameter for tool SQLite to tabular",
262 "name": "sqlitedb"
263 }
264 ],
265 "label": null,
266 "name": "SQLite to tabular",
267 "outputs": [
268 {
269 "name": "query_results",
270 "type": "tabular"
271 }
272 ],
273 "position": {
274 "left": 874,
275 "top": 204
276 },
277 "post_job_actions": {
278 "RenameDatasetActionquery_results": {
279 "action_arguments": {
280 "newname": "MOLECULAR FUNCTION COMPARISON"
281 },
282 "action_type": "RenameDatasetAction",
283 "output_name": "query_results"
284 }
285 },
286 "tool_errors": null,
287 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
288 "tool_shed_repository": {
289 "changeset_revision": "78e9570fbe08",
290 "name": "sqlite_to_tabular",
291 "owner": "jjohnson",
292 "tool_shed": "toolshed.g2.bx.psu.edu"
293 },
294 "tool_state": "{\"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\",count(distinct c.peptide) as \\\\\\\"chukchi_peptides\\\\\\\", count(distinct b.id)*1.42 as \\\\\\\"bering_psms\\\\\\\", count(distinct c.id) as \\\\\\\"chukchi_psms\\\\\\\"\\\\nFROM go as g LEFT OUTER JOIN\\\\n ( SELECT go.description, bering.peptide, bering_psms.id\\\\n FROM go LEFT OUTER JOIN bering ON go.go_id = bering.go_reference JOIN bering_psms ON bering.peptide = bering_psms.sequence\\\\n GROUP BY go.description, bering.peptide, bering_psms.id\\\\n ) as b ON g.description = b.description LEFT OUTER JOIN\\\\n ( SELECT go.description, chukchi.peptide, chukchi_psms.id\\\\n FROM go LEFT OUTER JOIN chukchi ON go.go_id = chukchi.go_reference JOIN chukchi_psms ON chukchi.peptide = chukchi_psms.sequence\\\\n GROUP BY go.description, chukchi.peptide, chukchi_psms.id\\\\n ) as c ON g.description = c.description\\\\nWHERE g.aspect = 'molecular_function'\\\\nGROUP BY g.description\\\\nORDER BY abs(bering_peptides - chukchi_peptides) desc, bering_peptides desc,chukchi_peptides desc\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}",
295 "tool_version": "0.0.1",
296 "type": "tool",
297 "uuid": "ee7d5bd3-d2c4-4653-bd55-fa236abfc7f8",
298 "workflow_outputs": [
299 {
300 "label": null,
301 "output_name": "query_results",
302 "uuid": "90cf3457-65be-474d-a43f-ead52ad50e21"
303 }
304 ]
305 },
306 "7": {
307 "annotation": "",
308 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
309 "id": 7,
310 "input_connections": {
311 "sqlitedb": {
312 "id": 5,
313 "output_name": "sqlitedb"
314 }
315 },
316 "inputs": [
317 {
318 "description": "runtime parameter for tool SQLite to tabular",
319 "name": "sqlitedb"
320 }
321 ],
322 "label": null,
323 "name": "SQLite to tabular",
324 "outputs": [
325 {
326 "name": "query_results",
327 "type": "tabular"
328 }
329 ],
330 "position": {
331 "left": 876,
332 "top": 342
333 },
334 "post_job_actions": {
335 "RenameDatasetActionquery_results": {
336 "action_arguments": {
337 "newname": "CELLULAR COMPONENT COMPARISON"
338 },
339 "action_type": "RenameDatasetAction",
340 "output_name": "query_results"
341 }
342 },
343 "tool_errors": null,
344 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
345 "tool_shed_repository": {
346 "changeset_revision": "78e9570fbe08",
347 "name": "sqlite_to_tabular",
348 "owner": "jjohnson",
349 "tool_shed": "toolshed.g2.bx.psu.edu"
350 },
351 "tool_state": "{\"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\",count(distinct c.peptide) as \\\\\\\"chukchi_peptides\\\\\\\", count(distinct b.id)*1.42 as \\\\\\\"bering_psms\\\\\\\", count(distinct c.id) as \\\\\\\"chukchi_psms\\\\\\\"\\\\nFROM go as g LEFT OUTER JOIN\\\\n ( SELECT go.description, bering.peptide, bering_psms.id\\\\n FROM go LEFT OUTER JOIN bering ON go.go_id = bering.go_reference JOIN bering_psms ON bering.peptide = bering_psms.sequence\\\\n GROUP BY go.description, bering.peptide, bering_psms.id\\\\n ) as b ON g.description = b.description LEFT OUTER JOIN\\\\n ( SELECT go.description, chukchi.peptide, chukchi_psms.id\\\\n FROM go LEFT OUTER JOIN chukchi ON go.go_id = chukchi.go_reference JOIN chukchi_psms ON chukchi.peptide = chukchi_psms.sequence\\\\n GROUP BY go.description, chukchi.peptide, chukchi_psms.id\\\\n ) as c ON g.description = c.description\\\\nWHERE g.aspect = 'cellular_component'\\\\nGROUP BY g.description\\\\nORDER BY abs(bering_peptides - chukchi_peptides) desc, bering_peptides desc,chukchi_peptides desc\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}",
352 "tool_version": "0.0.1",
353 "type": "tool",
354 "uuid": "d0f27344-2721-47e3-891a-0a9288293945",
355 "workflow_outputs": [
356 {
357 "label": null,
358 "output_name": "query_results",
359 "uuid": "80f8307d-68d7-4a49-bae8-b43957dd3098"
360 }
361 ]
362 },
363 "8": {
364 "annotation": "",
365 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
366 "id": 8,
367 "input_connections": {
368 "sqlitedb": {
369 "id": 5,
370 "output_name": "sqlitedb"
371 }
372 },
373 "inputs": [
374 {
375 "description": "runtime parameter for tool SQLite to tabular",
376 "name": "sqlitedb"
377 }
378 ],
379 "label": null,
380 "name": "SQLite to tabular",
381 "outputs": [
382 {
383 "name": "query_results",
384 "type": "tabular"
385 }
386 ],
387 "position": {
388 "left": 883,
389 "top": 457.5
390 },
391 "post_job_actions": {
392 "RenameDatasetActionquery_results": {
393 "action_arguments": {
394 "newname": "PEPTIDE PSM COUNTS COMPARISON"
395 },
396 "action_type": "RenameDatasetAction",
397 "output_name": "query_results"
398 }
399 },
400 "tool_errors": null,
401 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
402 "tool_shed_repository": {
403 "changeset_revision": "78e9570fbe08",
404 "name": "sqlite_to_tabular",
405 "owner": "jjohnson",
406 "tool_shed": "toolshed.g2.bx.psu.edu"
407 },
408 "tool_state": "{\"sqlquery\": \"\\\"SELECT peptides.peptide, count(bering_psms.id)*1.42 as \\\\\\\"BeringStrait_PSMs\\\\\\\", count(chukchi_psms.id) as \\\\\\\"ChukchiSea_PSMs\\\\\\\"\\\\nFROM \\\\n(SELECT distinct sequence \\\\\\\"peptide\\\\\\\" FROM bering_psms UNION SELECT sequence as \\\\\\\"peptide\\\\\\\" FROM chukchi_psms) as peptides\\\\nLEFT JOIN bering_psms ON peptides.peptide = bering_psms.sequence\\\\nLEFT JOIN chukchi_psms ON peptides.peptide = chukchi_psms.sequence\\\\nGROUP BY peptides.peptide\\\\nORDER BY peptides.peptide\\\\n\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}",
409 "tool_version": "0.0.1",
410 "type": "tool",
411 "uuid": "a3b80420-6655-4acf-b62b-dcb4ac5d9c6e",
412 "workflow_outputs": [
413 {
414 "label": null,
415 "output_name": "query_results",
416 "uuid": "a9b9c19b-8ab2-4f08-9c1f-73e6991f58f9"
417 }
418 ]
419 }
420 },
421 "uuid": "9f54fdad-4b9b-4389-8c3a-4512f0cf8df5"
422 }