Mercurial > repos > galaxyp > abrf2017_workshop

comparison Galaxy-Workflow-ABRF_UNIPEPT__Peptide_GO_Summary_Step2.ga @ 1:338a6d724774 draft default tip

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 e81bd1614788b8bfe8752c4a4279abdcc34e9777
author galaxyp
date Thu, 16 Mar 2017 08:45:23 -0400
parents
children
comparison
equal deleted inserted replaced
0:eb71034189fb 1:338a6d724774
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "ABRF UNIPEPT: Peptide GO Summary Step2",
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": 193,
23 "top": 231.5
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": "60bd46b9-2911-4a36-94ac-e51e66a9a6e2",
31 "workflow_outputs": [
32 {
33 "label": null,
34 "output_name": "output",
35 "uuid": "7a0ce548-f4a1-4cf9-8e0c-2cc4092eb6cd"
36 }
37 ]
38 },
39 "1": {
40 "annotation": "",
41 "content_id": null,
42 "id": 1,
43 "input_connections": {},
44 "inputs": [
45 {
46 "description": "",
47 "name": "Sample 1 Pept2Prot (extra fields) Normalized"
48 }
49 ],
50 "label": null,
51 "name": "Input dataset",
52 "outputs": [],
53 "position": {
54 "left": 195,
55 "top": 310.5
56 },
57 "tool_errors": null,
58 "tool_id": null,
59 "tool_state": "{\"name\": \"Sample 1 Pept2Prot (extra fields) Normalized\"}",
60 "tool_version": null,
61 "type": "data_input",
62 "uuid": "52b44ffd-15ff-421b-977a-6b9a512d1582",
63 "workflow_outputs": [
64 {
65 "label": null,
66 "output_name": "output",
67 "uuid": "5d5337c5-f228-4054-92cf-f3e800f2a666"
68 }
69 ]
70 },
71 "2": {
72 "annotation": "",
73 "content_id": null,
74 "id": 2,
75 "input_connections": {},
76 "inputs": [
77 {
78 "description": "",
79 "name": "Sample 1 PSM Report"
80 }
81 ],
82 "label": null,
83 "name": "Input dataset",
84 "outputs": [],
85 "position": {
86 "left": 197,
87 "top": 386.5
88 },
89 "tool_errors": null,
90 "tool_id": null,
91 "tool_state": "{\"name\": \"Sample 1 PSM Report\"}",
92 "tool_version": null,
93 "type": "data_input",
94 "uuid": "2c906b80-b425-4280-9743-4151b15fd3f4",
95 "workflow_outputs": [
96 {
97 "label": null,
98 "output_name": "output",
99 "uuid": "ba24d136-484f-49c8-964f-982b56b26217"
100 }
101 ]
102 },
103 "3": {
104 "annotation": "",
105 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0",
106 "id": 3,
107 "input_connections": {
108 "tables_0|table": {
109 "id": 0,
110 "output_name": "output"
111 },
112 "tables_1|table": {
113 "id": 1,
114 "output_name": "output"
115 },
116 "tables_2|table": {
117 "id": 2,
118 "output_name": "output"
119 }
120 },
121 "inputs": [
122 {
123 "description": "runtime parameter for tool Query Tabular",
124 "name": "add_to_database"
125 }
126 ],
127 "label": null,
128 "name": "Query Tabular",
129 "outputs": [
130 {
131 "name": "sqlitedb",
132 "type": "sqlite"
133 },
134 {
135 "name": "output",
136 "type": "tabular"
137 }
138 ],
139 "position": {
140 "left": 442,
141 "top": 230
142 },
143 "post_job_actions": {
144 "RenameDatasetActionoutput": {
145 "action_arguments": {
146 "newname": "Bering Strait BIOLOGICAL PROCESS"
147 },
148 "action_type": "RenameDatasetAction",
149 "output_name": "output"
150 }
151 },
152 "tool_errors": null,
153 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0",
154 "tool_shed_repository": {
155 "changeset_revision": "e84d1c3bf4fe",
156 "name": "query_tabular",
157 "owner": "jjohnson",
158 "tool_shed": "toolshed.g2.bx.psu.edu"
159 },
160 "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\\\": \\\"true\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"bering_psms\\\", \\\"col_names\\\": \\\"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\", \\\"indexes\\\": []}, \\\"__index__\\\": 2, \\\"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 b.id) as \\\\\\\"bering_psms\\\\\\\"\\\\n FROM go as g 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 \\\\nWHERE g.aspect = 'biological_process'\\\\nGROUP BY g.description\\\\nORDER BY bering_peptides desc,bering_psms desc\\\\n\\\"\", \"add_to_database\": \"{\\\"withdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"workdb\": \"\\\"workdb.sqlite\\\"\"}",
161 "tool_version": "2.0.0",
162 "type": "tool",
163 "uuid": "8f335601-0ed2-4da1-8d51-3ad443f71400",
164 "workflow_outputs": [
165 {
166 "label": null,
167 "output_name": "output",
168 "uuid": "e662208f-4587-4b09-9e15-ccc7abb7268a"
169 },
170 {
171 "label": null,
172 "output_name": "sqlitedb",
173 "uuid": "4b685349-25cb-4459-9950-6207b94bafe6"
174 }
175 ]
176 },
177 "4": {
178 "annotation": "",
179 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
180 "id": 4,
181 "input_connections": {
182 "sqlitedb": {
183 "id": 3,
184 "output_name": "sqlitedb"
185 }
186 },
187 "inputs": [
188 {
189 "description": "runtime parameter for tool SQLite to tabular",
190 "name": "sqlitedb"
191 }
192 ],
193 "label": null,
194 "name": "SQLite to tabular",
195 "outputs": [
196 {
197 "name": "query_results",
198 "type": "tabular"
199 }
200 ],
201 "position": {
202 "left": 874,
203 "top": 204
204 },
205 "post_job_actions": {
206 "RenameDatasetActionquery_results": {
207 "action_arguments": {
208 "newname": "Bering Strait MOLECULAR FUNCTION"
209 },
210 "action_type": "RenameDatasetAction",
211 "output_name": "query_results"
212 }
213 },
214 "tool_errors": null,
215 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
216 "tool_shed_repository": {
217 "changeset_revision": "123b9ca5e26a",
218 "name": "sqlite_to_tabular",
219 "owner": "jjohnson",
220 "tool_shed": "toolshed.g2.bx.psu.edu"
221 },
222 "tool_state": "{\"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\", count(distinct b.id) as \\\\\\\"bering_psms\\\\\\\" \\\\nFROM go as g 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 \\\\nWHERE g.aspect = 'molecular_function'\\\\nGROUP BY g.description\\\\nORDER BY bering_peptides desc,bering_psms desc\\\\n\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}",
223 "tool_version": "0.0.1",
224 "type": "tool",
225 "uuid": "ff3593c9-a8eb-4b26-858d-e156de462541",
226 "workflow_outputs": [
227 {
228 "label": null,
229 "output_name": "query_results",
230 "uuid": "4fd55eff-0f1e-47f2-b4aa-da2ebc91bcda"
231 }
232 ]
233 },
234 "5": {
235 "annotation": "",
236 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
237 "id": 5,
238 "input_connections": {
239 "sqlitedb": {
240 "id": 3,
241 "output_name": "sqlitedb"
242 }
243 },
244 "inputs": [
245 {
246 "description": "runtime parameter for tool SQLite to tabular",
247 "name": "sqlitedb"
248 }
249 ],
250 "label": null,
251 "name": "SQLite to tabular",
252 "outputs": [
253 {
254 "name": "query_results",
255 "type": "tabular"
256 }
257 ],
258 "position": {
259 "left": 876,
260 "top": 342
261 },
262 "post_job_actions": {
263 "RenameDatasetActionquery_results": {
264 "action_arguments": {
265 "newname": "Bering Strait CELLULAR COMPONENT"
266 },
267 "action_type": "RenameDatasetAction",
268 "output_name": "query_results"
269 }
270 },
271 "tool_errors": null,
272 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
273 "tool_shed_repository": {
274 "changeset_revision": "123b9ca5e26a",
275 "name": "sqlite_to_tabular",
276 "owner": "jjohnson",
277 "tool_shed": "toolshed.g2.bx.psu.edu"
278 },
279 "tool_state": "{\"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\", count(distinct b.id) as \\\\\\\"bering_psms\\\\\\\" \\\\nFROM go as g 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 \\\\nWHERE g.aspect = 'cellular_component'\\\\nGROUP BY g.description\\\\nORDER BY bering_peptides desc,bering_psms desc\\\\n\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}",
280 "tool_version": "0.0.1",
281 "type": "tool",
282 "uuid": "4aadf296-0c45-43bb-a146-e267c2955233",
283 "workflow_outputs": [
284 {
285 "label": null,
286 "output_name": "query_results",
287 "uuid": "6042e237-57f6-489e-b8a7-5d32afd39d5e"
288 }
289 ]
290 },
291 "6": {
292 "annotation": "",
293 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
294 "id": 6,
295 "input_connections": {
296 "sqlitedb": {
297 "id": 3,
298 "output_name": "sqlitedb"
299 }
300 },
301 "inputs": [
302 {
303 "description": "runtime parameter for tool SQLite to tabular",
304 "name": "sqlitedb"
305 }
306 ],
307 "label": null,
308 "name": "SQLite to tabular",
309 "outputs": [
310 {
311 "name": "query_results",
312 "type": "tabular"
313 }
314 ],
315 "position": {
316 "left": 882,
317 "top": 458.5
318 },
319 "post_job_actions": {
320 "RenameDatasetActionquery_results": {
321 "action_arguments": {
322 "newname": "Bering Strait PEPTIDES and PSMs"
323 },
324 "action_type": "RenameDatasetAction",
325 "output_name": "query_results"
326 }
327 },
328 "tool_errors": null,
329 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
330 "tool_shed_repository": {
331 "changeset_revision": "123b9ca5e26a",
332 "name": "sqlite_to_tabular",
333 "owner": "jjohnson",
334 "tool_shed": "toolshed.g2.bx.psu.edu"
335 },
336 "tool_state": "{\"sqlquery\": \"\\\"SELECT sequence as \\\\\\\"peptide\\\\\\\", count(id) as \\\\\\\"PSMs\\\\\\\"\\\\nFROM bering_psms\\\\nWHERE validation IS NOT 'Confident' AND confidence >= 95\\\\nGROUP BY sequence\\\\nORDER BY sequence\\\\n\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}",
337 "tool_version": "0.0.1",
338 "type": "tool",
339 "uuid": "e172020f-dd58-4027-9d6c-94273ec2aee8",
340 "workflow_outputs": [
341 {
342 "label": null,
343 "output_name": "query_results",
344 "uuid": "291d94c5-9ff7-44ae-872f-76955c56d6f4"
345 }
346 ]
347 }
348 },
349 "uuid": "57999e7e-0de6-41e0-87d3-1660414d9896"
350 }