Mercurial > repos > peterjc > secreted_protein_workflow

comparison secreted_protein_workflow.ga @ 0:3a6de5cb858d draft

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Uploaded first attempt at a workflow with dependencies on the Tool Shed
author peterjc
date Mon, 06 May 2013 11:11:11 -0400
parents
children 36b2c2b5051e
comparison
equal deleted inserted replaced
-1:000000000000 0:3a6de5cb858d
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "Runs SignalP v3.0 and TMHMM v2.0 to look for secreted proteins.",
4 "format-version": "0.1",
5 "name": "Find secreted proteins with TMHMM and SignalP",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "",
14 "name": "Input Dataset"
15 }
16 ],
17 "name": "Input dataset",
18 "outputs": [],
19 "position": {
20 "left": 200,
21 "top": 200
22 },
23 "tool_errors": null,
24 "tool_id": null,
25 "tool_state": "{\"name\": \"Input Dataset\"}",
26 "tool_version": null,
27 "type": "data_input",
28 "user_outputs": []
29 },
30 "1": {
31 "annotation": "",
32 "id": 1,
33 "input_connections": {
34 "fasta_file": {
35 "id": 0,
36 "output_name": "output"
37 }
38 },
39 "inputs": [
40 {
41 "description": "runtime parameter for tool SignalP 3.0",
42 "name": "organism"
43 }
44 ],
45 "name": "SignalP 3.0",
46 "outputs": [
47 {
48 "name": "tabular_file",
49 "type": "tabular"
50 }
51 ],
52 "position": {
53 "left": 240,
54 "top": 341
55 },
56 "post_job_actions": {
57 "HideDatasetActiontabular_file": {
58 "action_arguments": {},
59 "action_type": "HideDatasetAction",
60 "output_name": "tabular_file"
61 }
62 },
63 "tool_errors": null,
64 "tool_id": "signalp3",
65 "tool_state": "{\"organism\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"truncate\": \"\\\"60\\\"\", \"__page__\": 0}",
66 "tool_version": "0.0.8",
67 "type": "tool",
68 "user_outputs": []
69 },
70 "2": {
71 "annotation": "Select proteins with predicted signal peptide (SignalP NN D-Score or HMM)",
72 "id": 2,
73 "input_connections": {
74 "input": {
75 "id": 1,
76 "output_name": "tabular_file"
77 }
78 },
79 "inputs": [],
80 "name": "Filter",
81 "outputs": [
82 {
83 "name": "out_file1",
84 "type": "input"
85 }
86 ],
87 "position": {
88 "left": 323,
89 "top": 528
90 },
91 "post_job_actions": {
92 "HideDatasetActionout_file1": {
93 "action_arguments": {},
94 "action_type": "HideDatasetAction",
95 "output_name": "out_file1"
96 },
97 "RenameDatasetActionout_file1": {
98 "action_arguments": {
99 "newname": "Filtered SignalP results"
100 },
101 "action_type": "RenameDatasetAction",
102 "output_name": "out_file1"
103 }
104 },
105 "tool_errors": null,
106 "tool_id": "Filter1",
107 "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c14=='Y' or c15=='S'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}",
108 "tool_version": "1.1.0",
109 "type": "tool",
110 "user_outputs": []
111 },
112 "3": {
113 "annotation": "Select those sequences with signal peptides.",
114 "id": 3,
115 "input_connections": {
116 "input_file": {
117 "id": 0,
118 "output_name": "output"
119 },
120 "input_tabular": {
121 "id": 2,
122 "output_name": "out_file1"
123 }
124 },
125 "inputs": [],
126 "name": "Filter sequences by ID",
127 "outputs": [
128 {
129 "name": "output_pos",
130 "type": "fasta"
131 },
132 {
133 "name": "output_neg",
134 "type": "fasta"
135 }
136 ],
137 "position": {
138 "left": 527,
139 "top": 200
140 },
141 "post_job_actions": {
142 "HideDatasetActionoutput_neg": {
143 "action_arguments": {},
144 "action_type": "HideDatasetAction",
145 "output_name": "output_neg"
146 },
147 "HideDatasetActionoutput_pos": {
148 "action_arguments": {},
149 "action_type": "HideDatasetAction",
150 "output_name": "output_pos"
151 }
152 },
153 "tool_errors": null,
154 "tool_id": "seq_filter_by_id",
155 "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}",
156 "tool_version": "0.0.1",
157 "type": "tool",
158 "user_outputs": []
159 },
160 "4": {
161 "annotation": "",
162 "id": 4,
163 "input_connections": {
164 "fasta_file": {
165 "id": 3,
166 "output_name": "output_pos"
167 }
168 },
169 "inputs": [],
170 "name": "TMHMM 2.0",
171 "outputs": [
172 {
173 "name": "tabular_file",
174 "type": "tabular"
175 }
176 ],
177 "position": {
178 "left": 643,
179 "top": 443
180 },
181 "post_job_actions": {
182 "HideDatasetActiontabular_file": {
183 "action_arguments": {},
184 "action_type": "HideDatasetAction",
185 "output_name": "tabular_file"
186 }
187 },
188 "tool_errors": null,
189 "tool_id": "tmhmm2",
190 "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
191 "tool_version": "0.0.7",
192 "type": "tool",
193 "user_outputs": []
194 },
195 "5": {
196 "annotation": "Select proteins with no predicted transmembrane helices.",
197 "id": 5,
198 "input_connections": {
199 "input": {
200 "id": 4,
201 "output_name": "tabular_file"
202 }
203 },
204 "inputs": [],
205 "name": "Filter",
206 "outputs": [
207 {
208 "name": "out_file1",
209 "type": "input"
210 }
211 ],
212 "position": {
213 "left": 729,
214 "top": 566
215 },
216 "post_job_actions": {
217 "HideDatasetActionout_file1": {
218 "action_arguments": {},
219 "action_type": "HideDatasetAction",
220 "output_name": "out_file1"
221 },
222 "RenameDatasetActionout_file1": {
223 "action_arguments": {
224 "newname": "Filtered TMHMM results"
225 },
226 "action_type": "RenameDatasetAction",
227 "output_name": "out_file1"
228 }
229 },
230 "tool_errors": null,
231 "tool_id": "Filter1",
232 "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c5== 0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}",
233 "tool_version": "1.1.0",
234 "type": "tool",
235 "user_outputs": []
236 },
237 "6": {
238 "annotation": "Select those sequences with no transmembrane helices (from those with signal peptides).",
239 "id": 6,
240 "input_connections": {
241 "input_file": {
242 "id": 3,
243 "output_name": "output_pos"
244 },
245 "input_tabular": {
246 "id": 5,
247 "output_name": "out_file1"
248 }
249 },
250 "inputs": [],
251 "name": "Filter sequences by ID",
252 "outputs": [
253 {
254 "name": "output_pos",
255 "type": "fasta"
256 },
257 {
258 "name": "output_neg",
259 "type": "fasta"
260 }
261 ],
262 "position": {
263 "left": 893,
264 "top": 281
265 },
266 "post_job_actions": {
267 "HideDatasetActionoutput_neg": {
268 "action_arguments": {},
269 "action_type": "HideDatasetAction",
270 "output_name": "output_neg"
271 },
272 "RenameDatasetActionoutput_pos": {
273 "action_arguments": {
274 "newname": "Secreted proteins"
275 },
276 "action_type": "RenameDatasetAction",
277 "output_name": "output_pos"
278 }
279 },
280 "tool_errors": null,
281 "tool_id": "seq_filter_by_id",
282 "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}",
283 "tool_version": "0.0.1",
284 "type": "tool",
285 "user_outputs": []
286 }
287 }
288 }