Mercurial > repos > galaxyp > abrf2017_workshop

comparison Galaxy-Workflow-ABRF_UNIPEPT_Taxonomy_Workflow_Bering_Strait.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 UNIPEPT:Taxonomy Workflow Bering Strait",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "content_id": null,
10 "id": 0,
11 "input_connections": {},
12 "inputs": [
13 {
14 "description": "",
15 "name": "PSM Report"
16 }
17 ],
18 "label": null,
19 "name": "Input dataset",
20 "outputs": [],
21 "position": {
22 "left": 189,
23 "top": 163
24 },
25 "tool_errors": null,
26 "tool_id": null,
27 "tool_state": "{\"name\": \"PSM Report\"}",
28 "tool_version": null,
29 "type": "data_input",
30 "uuid": "22470252-89e0-47c6-ba28-5efab1803316",
31 "workflow_outputs": [
32 {
33 "label": null,
34 "output_name": "output",
35 "uuid": "8c57d953-0eca-4d62-8e5c-2ad994f7db4b"
36 }
37 ]
38 },
39 "1": {
40 "annotation": "",
41 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0",
42 "id": 1,
43 "input_connections": {
44 "tables_0|table": {
45 "id": 0,
46 "output_name": "output"
47 }
48 },
49 "inputs": [
50 {
51 "description": "runtime parameter for tool Query Tabular",
52 "name": "add_to_database"
53 }
54 ],
55 "label": null,
56 "name": "Query Tabular",
57 "outputs": [
58 {
59 "name": "sqlitedb",
60 "type": "sqlite"
61 },
62 {
63 "name": "output",
64 "type": "tabular"
65 }
66 ],
67 "position": {
68 "left": 397,
69 "top": 295
70 },
71 "post_job_actions": {
72 "HideDatasetActionsqlitedb": {
73 "action_arguments": {},
74 "action_type": "HideDatasetAction",
75 "output_name": "sqlitedb"
76 }
77 },
78 "tool_errors": null,
79 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0",
80 "tool_shed_repository": {
81 "changeset_revision": "ae27dab228b8",
82 "name": "query_tabular",
83 "owner": "jjohnson",
84 "tool_shed": "toolshed.g2.bx.psu.edu"
85 },
86 "tool_state": "{\"tables\": \"[{\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"true\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"psm\\\", \\\"col_names\\\": \\\"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\", \\\"indexes\\\": []}, \\\"__index__\\\": 0, \\\"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\": \"\\\"true\\\"\", \"sqlquery\": \"\\\"SELECT distinct sequence \\\\nFROM psm \\\\nWHERE validation IS NOT 'Confident' AND confidence >= 95 \\\\nORDER BY sequence\\\"\", \"add_to_database\": \"{\\\"withdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"workdb\": \"\\\"workdb.sqlite\\\"\"}",
87 "tool_version": "2.0.0",
88 "type": "tool",
89 "uuid": "b210efa3-4926-4e07-99e6-2619258d28a7",
90 "workflow_outputs": [
91 {
92 "label": "",
93 "output_name": "output",
94 "uuid": "15f7b9a0-5c26-4bbd-aa6b-e92746886a25"
95 }
96 ]
97 },
98 "2": {
99 "annotation": "",
100 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
101 "id": 2,
102 "input_connections": {
103 "sqlitedb": {
104 "id": 1,
105 "output_name": "sqlitedb"
106 }
107 },
108 "inputs": [
109 {
110 "description": "runtime parameter for tool SQLite to tabular",
111 "name": "sqlitedb"
112 }
113 ],
114 "label": null,
115 "name": "SQLite to tabular",
116 "outputs": [
117 {
118 "name": "query_results",
119 "type": "tabular"
120 }
121 ],
122 "position": {
123 "left": 760.5,
124 "top": 265.5
125 },
126 "post_job_actions": {
127 "RenameDatasetActionquery_results": {
128 "action_arguments": {
129 "newname": "Bering Strait PEPTIDEs with PSMs"
130 },
131 "action_type": "RenameDatasetAction",
132 "output_name": "query_results"
133 }
134 },
135 "tool_errors": null,
136 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1",
137 "tool_shed_repository": {
138 "changeset_revision": "78e9570fbe08",
139 "name": "sqlite_to_tabular",
140 "owner": "jjohnson",
141 "tool_shed": "toolshed.g2.bx.psu.edu"
142 },
143 "tool_state": "{\"sqlquery\": \"\\\"SELECT sequence as \\\\\\\"peptide\\\\\\\", count(id) as \\\\\\\"PSMs\\\\\\\"\\\\nFROM psm \\\\nWHERE validation IS NOT 'Confident' AND confidence >= 95 \\\\nGROUP BY sequence\\\\nORDER BY sequence\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}",
144 "tool_version": "0.0.1",
145 "type": "tool",
146 "uuid": "070a98b8-b69e-442d-94da-f0f99cf397f9",
147 "workflow_outputs": [
148 {
149 "label": null,
150 "output_name": "query_results",
151 "uuid": "11c53e11-5c81-41a3-af8b-9b90ccb6b45c"
152 }
153 ]
154 },
155 "3": {
156 "annotation": "",
157 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1",
158 "id": 3,
159 "input_connections": {
160 "peptide_src|input_tsv": {
161 "id": 1,
162 "output_name": "output"
163 }
164 },
165 "inputs": [
166 {
167 "description": "runtime parameter for tool Unipept",
168 "name": "peptide_src"
169 }
170 ],
171 "label": null,
172 "name": "Unipept",
173 "outputs": [
174 {
175 "name": "output_json",
176 "type": "d3_hierarchy"
177 },
178 {
179 "name": "output_tsv",
180 "type": "tabular"
181 },
182 {
183 "name": "output_csv",
184 "type": "csv"
185 },
186 {
187 "name": "output_unmatched",
188 "type": "tabular"
189 }
190 ],
191 "position": {
192 "left": 732.5,
193 "top": 367.5
194 },
195 "post_job_actions": {
196 "HideDatasetActionoutput_csv": {
197 "action_arguments": {},
198 "action_type": "HideDatasetAction",
199 "output_name": "output_csv"
200 },
201 "HideDatasetActionoutput_unmatched": {
202 "action_arguments": {},
203 "action_type": "HideDatasetAction",
204 "output_name": "output_unmatched"
205 },
206 "RenameDatasetActionoutput_json": {
207 "action_arguments": {
208 "newname": "Unipept: TAXONOMY Phylogenetic Tree (Bering Strait)"
209 },
210 "action_type": "RenameDatasetAction",
211 "output_name": "output_json"
212 }
213 },
214 "tool_errors": null,
215 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1",
216 "tool_shed_repository": {
217 "changeset_revision": "34758ab8aaa4",
218 "name": "unipept",
219 "owner": "galaxyp",
220 "tool_shed": "toolshed.g2.bx.psu.edu"
221 },
222 "tool_state": "{\"__page__\": 0, \"outputs\": \"[\\\"tsv\\\", \\\"json\\\"]\", \"__rerun_remap_job_id__\": null, \"peptide_src\": \"{\\\"column\\\": \\\"1\\\", \\\"fmt\\\": \\\"tabular\\\", \\\"input_tsv\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\", \"strict\": \"\\\"false\\\"\", \"unipept\": \"{\\\"allfields\\\": \\\"false\\\", \\\"extra\\\": \\\"false\\\", \\\"api\\\": \\\"pept2lca\\\", \\\"names\\\": \\\"true\\\", \\\"__current_case__\\\": 0, \\\"equate_il\\\": \\\"true\\\"}\"}",
223 "tool_version": "2.0.1",
224 "type": "tool",
225 "uuid": "6163af00-e4d8-4aa8-8dd8-27d0f99489db",
226 "workflow_outputs": [
227 {
228 "label": null,
229 "output_name": "output_tsv",
230 "uuid": "11b0f0a3-066b-4680-8628-927277c3bb57"
231 },
232 {
233 "label": null,
234 "output_name": "output_json",
235 "uuid": "885b932a-4e21-40cf-a687-3075adcbbd9f"
236 }
237 ]
238 },
239 "4": {
240 "annotation": "",
241 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0",
242 "id": 4,
243 "input_connections": {
244 "tables_0|table": {
245 "id": 0,
246 "output_name": "output"
247 },
248 "tables_1|table": {
249 "id": 3,
250 "output_name": "output_tsv"
251 }
252 },
253 "inputs": [
254 {
255 "description": "runtime parameter for tool Query Tabular",
256 "name": "add_to_database"
257 }
258 ],
259 "label": null,
260 "name": "Query Tabular",
261 "outputs": [
262 {
263 "name": "sqlitedb",
264 "type": "sqlite"
265 },
266 {
267 "name": "output",
268 "type": "tabular"
269 }
270 ],
271 "position": {
272 "left": 1044,
273 "top": 162
274 },
275 "post_job_actions": {
276 "HideDatasetActionsqlitedb": {
277 "action_arguments": {},
278 "action_type": "HideDatasetAction",
279 "output_name": "sqlitedb"
280 },
281 "RenameDatasetActionoutput": {
282 "action_arguments": {
283 "newname": "Unipept: TAXONOMY GENUS PSMs Peptides (Bering Strait)"
284 },
285 "action_type": "RenameDatasetAction",
286 "output_name": "output"
287 }
288 },
289 "tool_errors": null,
290 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0",
291 "tool_shed_repository": {
292 "changeset_revision": "ae27dab228b8",
293 "name": "query_tabular",
294 "owner": "jjohnson",
295 "tool_shed": "toolshed.g2.bx.psu.edu"
296 },
297 "tool_state": "{\"tables\": \"[{\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"true\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"psm\\\", \\\"col_names\\\": \\\",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\", \\\"indexes\\\": []}, \\\"__index__\\\": 0, \\\"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\\\": \\\"lca\\\", \\\"col_names\\\": \\\"peptide,,,,,,,,,,,,,,,,,,,,,genus\\\", \\\"indexes\\\": []}, \\\"__index__\\\": 1, \\\"input_opts\\\": {\\\"linefilters\\\": [{\\\"filter\\\": {\\\"regex_action\\\": \\\"exclude_match\\\", \\\"regex_pattern\\\": \\\"#peptide\\\", \\\"__current_case__\\\": 2, \\\"filter_type\\\": \\\"regex\\\"}, \\\"__index__\\\": 0}]}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\", \"save_db\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\", \"sqlquery\": \"\\\"SELECT lca.genus,count(psm.sequence) as \\\\\\\"PSMs\\\\\\\",count(distinct psm.sequence) as \\\\\\\"DISTINCT PEPTIDES\\\\\\\" \\\\nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \\\\nWHERE validation IS NOT 'Confident' \\\\nAND confidence >= 95 \\\\nGROUP BY lca.genus \\\\nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc\\\"\", \"add_to_database\": \"{\\\"withdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"workdb\": \"\\\"workdb.sqlite\\\"\"}",
298 "tool_version": "2.0.0",
299 "type": "tool",
300 "uuid": "4ac60e8a-cc65-48c8-9ea5-a26b35b90558",
301 "workflow_outputs": [
302 {
303 "label": null,
304 "output_name": "output",
305 "uuid": "c618c51e-2f1e-437c-a570-981d2d07ea02"
306 }
307 ]
308 }
309 },
310 "uuid": "87aed6af-eb3b-4d42-99c0-e1a62fd59413"
311 }