Mercurial > repos > artbio > metavisitor_2_workflows

comparison Galaxy-Workflow-Metavisitor__Workflow_for_nucleic_vir2_generation.ga @ 0:c375489bbcb0 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows/metavisitor_2_workflows commit ecf95caa7d5e9ab001a75cbf5fb306e7ecd3def3
author artbio
date Sun, 21 Jul 2019 19:22:52 -0400
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-1:000000000000 0:c375489bbcb0
1 {
2 "a_galaxy_workflow": "true",
3 "uuid": "742e3aa8-0dc5-440d-8120-3b10f4e7308d",
4 "tags": [],
5 "format-version": "0.1",
6 "version": 1,
7 "steps": {
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10 "errors": null,
11 "uuid": "25b4eea6-c049-4432-9ebb-5b7c7a17e24b",
12 "tool_version": "2.3.0",
13 "outputs": [
14 {
15 "type": "fasta",
16 "name": "outfile"
17 },
18 {
19 "type": "txt",
20 "name": "logfile"
21 }
22 ],
23 "post_job_actions": {},
24 "workflow_outputs": [
25 {
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27 "uuid": "b5b6d8a1-5d12-4df9-97e3-f82124301e24",
28 "label": null
29 },
30 {
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32 "uuid": "8243ff90-8e45-4d12-b9d0-ea17ee0dd3c0",
33 "label": null
34 }
35 ],
36 "annotation": "sequences > 10 000bp",
37 "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/2.3.0",
38 "input_connections": {},
39 "inputs": [],
40 "position": {
41 "top": 563,
42 "left": 200
43 },
44 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"queryString\": \"\\\"txid10239[Organism] NOT txid131567[Organism] NOT phage[All Fields] NOT patent[All Fields] NOT chimeric[Title] NOT vector[Title] NOT method[Title] NOT X174[All Fields] AND 10001:1300000[Sequence length]\\\"\", \"dbname\": \"\\\"nuccore\\\"\", \"dry_run\": \"\\\"false\\\"\"}",
45 "label": "Get long sequences",
46 "type": "tool",
47 "id": 1,
48 "tool_shed_repository": {
49 "owner": "artbio",
50 "changeset_revision": "c667d0ee39f5",
51 "name": "fetch_fasta_from_ncbi",
52 "tool_shed": "toolshed.g2.bx.psu.edu"
53 },
54 "name": "Retrieve FASTA from NCBI"
55 },
56 "0": {
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58 "errors": null,
59 "uuid": "9c3e474c-3e57-4378-a5cc-ef9c6b7b092a",
60 "tool_version": "2.3.0",
61 "outputs": [
62 {
63 "type": "fasta",
64 "name": "outfile"
65 },
66 {
67 "type": "txt",
68 "name": "logfile"
69 }
70 ],
71 "post_job_actions": {},
72 "workflow_outputs": [
73 {
74 "output_name": "outfile",
75 "uuid": "f1d297ff-bf05-41ac-b262-4901674827a2",
76 "label": null
77 },
78 {
79 "output_name": "logfile",
80 "uuid": "b27a01c2-0d64-4aae-941d-946dd21e6bd2",
81 "label": null
82 }
83 ],
84 "annotation": "sequences <= 10 000bp",
85 "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/2.3.0",
86 "input_connections": {},
87 "inputs": [],
88 "position": {
89 "top": 241,
90 "left": 213
91 },
92 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"queryString\": \"\\\"txid10239[Organism] NOT txid131567[Organism] NOT phage[All Fields] NOT patent[All Fields] NOT chimeric[Title] NOT vector[Title] NOT method[Title] NOT X174[All Fields] AND 301:10000[Sequence length]\\\"\", \"dbname\": \"\\\"nuccore\\\"\", \"dry_run\": \"\\\"false\\\"\"}",
93 "label": "Get short sequences",
94 "type": "tool",
95 "id": 0,
96 "tool_shed_repository": {
97 "owner": "artbio",
98 "changeset_revision": "c667d0ee39f5",
99 "name": "fetch_fasta_from_ncbi",
100 "tool_shed": "toolshed.g2.bx.psu.edu"
101 },
102 "name": "Retrieve FASTA from NCBI"
103 },
104 "3": {
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106 "errors": null,
107 "uuid": "94beda09-1785-4da8-84ec-70773fa6eddd",
108 "tool_version": "1.4.1",
109 "outputs": [
110 {
111 "type": "input",
112 "name": "paired_output"
113 },
114 {
115 "type": "input",
116 "name": "list_output"
117 },
118 {
119 "type": "input",
120 "name": "out_file1"
121 },
122 {
123 "type": "_sniff_",
124 "name": "paired_out_file"
125 }
126 ],
127 "post_job_actions": {
128 "HideDatasetActionpaired_out_file": {
129 "output_name": "paired_out_file",
130 "action_type": "HideDatasetAction",
131 "action_arguments": {}
132 },
133 "RenameDatasetActionout_file1": {
134 "output_name": "out_file1",
135 "action_type": "RenameDatasetAction",
136 "action_arguments": {
137 "newname": "Vir2"
138 }
139 },
140 "HideDatasetActionpaired_output": {
141 "output_name": "paired_output",
142 "action_type": "HideDatasetAction",
143 "action_arguments": {}
144 },
145 "HideDatasetActionout_file1": {
146 "output_name": "out_file1",
147 "action_type": "HideDatasetAction",
148 "action_arguments": {}
149 },
150 "HideDatasetActionlist_output": {
151 "output_name": "list_output",
152 "action_type": "HideDatasetAction",
153 "action_arguments": {}
154 }
155 },
156 "workflow_outputs": [],
157 "annotation": "",
158 "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1",
159 "input_connections": {
160 "global_condition|inputs": [
161 {
162 "output_name": "centroids",
163 "id": 2
164 },
165 {
166 "output_name": "outfile",
167 "id": 1
168 }
169 ]
170 },
171 "inputs": [
172 {
173 "name": "global_condition",
174 "description": "runtime parameter for tool Concatenate multiple datasets"
175 }
176 ],
177 "position": {
178 "top": 571.5,
179 "left": 735
180 },
181 "tool_state": "{\"dataset_names\": \"\\\"false\\\"\", \"headers\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"global_condition\": \"{\\\"__current_case__\\\": 0, \\\"input_type\\\": \\\"singles\\\", \\\"inputs\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}",
182 "label": "Vir2",
183 "type": "tool",
184 "id": 3,
185 "tool_shed_repository": {
186 "owner": "artbio",
187 "changeset_revision": "55cf9d9defd1",
188 "name": "concatenate_multiple_datasets",
189 "tool_shed": "toolshed.g2.bx.psu.edu"
190 },
191 "name": "Concatenate multiple datasets"
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193 "2": {
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195 "errors": null,
196 "uuid": "6fddbef5-bc89-4574-a0cf-335aee053e4c",
197 "tool_version": "2.8.3.0",
198 "outputs": [
199 {
200 "type": "fasta",
201 "name": "msaout"
202 },
203 {
204 "type": "fasta",
205 "name": "consout"
206 },
207 {
208 "type": "fasta",
209 "name": "centroids"
210 },
211 {
212 "type": "fasta",
213 "name": "alnout"
214 },
215 {
216 "type": "fasta",
217 "name": "notmatched"
218 },
219 {
220 "type": "fasta",
221 "name": "matched"
222 },
223 {
224 "type": "tabular",
225 "name": "blast6out"
226 },
227 {
228 "type": "fasta",
229 "name": "fastapairs"
230 },
231 {
232 "type": "tabular",
233 "name": "uc_outfile"
234 }
235 ],
236 "post_job_actions": {
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238 "output_name": "fastapairs",
239 "action_type": "HideDatasetAction",
240 "action_arguments": {}
241 },
242 "HideDatasetActionconsout": {
243 "output_name": "consout",
244 "action_type": "HideDatasetAction",
245 "action_arguments": {}
246 },
247 "HideDatasetActionmsaout": {
248 "output_name": "msaout",
249 "action_type": "HideDatasetAction",
250 "action_arguments": {}
251 },
252 "HideDatasetActionalnout": {
253 "output_name": "alnout",
254 "action_type": "HideDatasetAction",
255 "action_arguments": {}
256 },
257 "HideDatasetActionblast6out": {
258 "output_name": "blast6out",
259 "action_type": "HideDatasetAction",
260 "action_arguments": {}
261 },
262 "HideDatasetActionuc_outfile": {
263 "output_name": "uc_outfile",
264 "action_type": "HideDatasetAction",
265 "action_arguments": {}
266 },
267 "HideDatasetActionnotmatched": {
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269 "action_type": "HideDatasetAction",
270 "action_arguments": {}
271 },
272 "HideDatasetActionmatched": {
273 "output_name": "matched",
274 "action_type": "HideDatasetAction",
275 "action_arguments": {}
276 }
277 },
278 "workflow_outputs": [
279 {
280 "output_name": "centroids",
281 "uuid": "091f386f-32e1-4270-8754-9da84c187b82",
282 "label": null
283 }
284 ],
285 "annotation": "",
286 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_clustering/2.8.3.0",
287 "input_connections": {
288 "infile": {
289 "output_name": "outfile",
290 "id": 0
291 }
292 },
293 "inputs": [
294 {
295 "name": "infile",
296 "description": "runtime parameter for tool VSearch clustering"
297 }
298 ],
299 "position": {
300 "top": 232,
301 "left": 463.5
302 },
303 "tool_state": "{\"sizein\": \"\\\"false\\\"\", \"cons_truncate\": \"\\\"false\\\"\", \"__page__\": null, \"maxrejects\": \"\\\"32\\\"\", \"usersort\": \"\\\"false\\\"\", \"qmask\": \"\\\"dust\\\"\", \"iddef\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"clustering_mode\": \"{\\\"__current_case__\\\": 0, \\\"clustering_mode_select\\\": \\\"cluster_fast\\\"}\", \"id\": \"\\\"0.95\\\"\", \"sizeout\": \"\\\"false\\\"\", \"strand\": \"\\\"plus\\\"\", \"outputs\": \"[\\\"--centroids\\\"]\", \"maxaccepts\": \"\\\"1\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"uc\": \"\\\"false\\\"\"}",
304 "label": "Get centroids",
305 "type": "tool",
306 "id": 2,
307 "tool_shed_repository": {
308 "owner": "iuc",
309 "changeset_revision": "b3c7199d8786",
310 "name": "vsearch",
311 "tool_shed": "toolshed.g2.bx.psu.edu"
312 },
313 "name": "VSearch clustering"
314 }
315 },
316 "annotation": "",
317 "name": "Metavisitor: Workflow for nucleic vir2 generation"
318 }