comparison Galaxy-Workflow-Estimate_minimum_informative_read_depth.ga @ 0:07588b899c13 draft

Uploaded
author arkarachai-fungtammasan
date Wed, 01 Apr 2015 17:05:51 -0400
parents
children d75894f5d61b
comparison
equal deleted inserted replaced
-1:000000000000 0:07588b899c13
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "Estimate minimum informative read depth",
6 "steps": {
7 "0": {
8 "annotation": "See sample in https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "See sample in https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files",
14 "name": "TR error rate"
15 }
16 ],
17 "name": "Input dataset",
18 "outputs": [],
19 "position": {
20 "left": 220,
21 "top": 737
22 },
23 "tool_errors": null,
24 "tool_id": null,
25 "tool_state": "{\"name\": \"TR error rate\"}",
26 "tool_version": null,
27 "type": "data_input",
28 "user_outputs": []
29 },
30 "1": {
31 "annotation": "replace 'A' with motif of interest",
32 "id": 1,
33 "input_connections": {
34 "input": {
35 "id": 0,
36 "output_name": "output"
37 }
38 },
39 "inputs": [],
40 "name": "Filter",
41 "outputs": [
42 {
43 "name": "out_file1",
44 "type": "input"
45 }
46 ],
47 "position": {
48 "left": 385,
49 "top": 260
50 },
51 "post_job_actions": {
52 "HideDatasetActionout_file1": {
53 "action_arguments": {},
54 "action_type": "HideDatasetAction",
55 "output_name": "out_file1"
56 }
57 },
58 "tool_errors": null,
59 "tool_id": "Filter1",
60 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c4=='A'\\\"\", \"__page__\": 0}",
61 "tool_version": "1.1.0",
62 "type": "tool",
63 "user_outputs": []
64 },
65 "2": {
66 "annotation": "",
67 "id": 2,
68 "input_connections": {
69 "error_profile": {
70 "id": 1,
71 "output_name": "out_file1"
72 }
73 },
74 "inputs": [],
75 "name": "Generate all possible combination of read profile",
76 "outputs": [
77 {
78 "name": "output",
79 "type": "tabular"
80 }
81 ],
82 "position": {
83 "left": 653.5,
84 "top": 203
85 },
86 "post_job_actions": {},
87 "tool_errors": null,
88 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/Profilegenerator/2.0.0",
89 "tool_state": "{\"error_profile\": \"null\", \"MOTIF\": \"\\\"A\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"minprob\": \"\\\"1e-08\\\"\", \"Maxdepth\": \"\\\"30\\\"\"}",
90 "tool_version": "2.0.0",
91 "type": "tool",
92 "user_outputs": []
93 },
94 "3": {
95 "annotation": "",
96 "id": 3,
97 "input_connections": {
98 "input": {
99 "id": 2,
100 "output_name": "output"
101 }
102 },
103 "inputs": [],
104 "name": "Unique",
105 "outputs": [
106 {
107 "name": "outfile",
108 "type": "input"
109 }
110 ],
111 "position": {
112 "left": 676,
113 "top": 322
114 },
115 "post_job_actions": {
116 "HideDatasetActionoutfile": {
117 "action_arguments": {},
118 "action_type": "HideDatasetAction",
119 "output_name": "outfile"
120 }
121 },
122 "tool_errors": null,
123 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
124 "tool_state": "{\"__page__\": 0, \"ignore_case\": \"\\\"False\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"is_numeric\": \"\\\"False\\\"\", \"input\": \"null\"}",
125 "tool_version": "0.3",
126 "type": "tool",
127 "user_outputs": []
128 },
129 "4": {
130 "annotation": "",
131 "id": 4,
132 "input_connections": {
133 "microsat_error_profile": {
134 "id": 0,
135 "output_name": "output"
136 },
137 "microsat_raw": {
138 "id": 3,
139 "output_name": "outfile"
140 }
141 },
142 "inputs": [],
143 "name": "Correct genotype for microsatellite errors",
144 "outputs": [
145 {
146 "name": "microsat_corrected",
147 "type": "tabular"
148 }
149 ],
150 "position": {
151 "left": 661,
152 "top": 427
153 },
154 "post_job_actions": {
155 "HideDatasetActionmicrosat_corrected": {
156 "action_arguments": {},
157 "action_type": "HideDatasetAction",
158 "output_name": "microsat_corrected"
159 }
160 },
161 "tool_errors": null,
162 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/GenotypeSTR/2.0.0",
163 "tool_state": "{\"microsat_raw\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"microsat_error_profile\": \"null\", \"expectedminorallele\": \"\\\"0.5\\\"\"}",
164 "tool_version": "2.0.0",
165 "type": "tool",
166 "user_outputs": []
167 },
168 "5": {
169 "annotation": "",
170 "id": 5,
171 "input_connections": {
172 "input": {
173 "id": 4,
174 "output_name": "microsat_corrected"
175 }
176 },
177 "inputs": [],
178 "name": "Select",
179 "outputs": [
180 {
181 "name": "out_file1",
182 "type": "input"
183 }
184 ],
185 "position": {
186 "left": 732,
187 "top": 629
188 },
189 "post_job_actions": {
190 "HideDatasetActionout_file1": {
191 "action_arguments": {},
192 "action_type": "HideDatasetAction",
193 "output_name": "out_file1"
194 }
195 },
196 "tool_errors": null,
197 "tool_id": "Grep1",
198 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"pattern\": \"\\\"hetero\\\"\"}",
199 "tool_version": "1.0.1",
200 "type": "tool",
201 "user_outputs": []
202 },
203 "6": {
204 "annotation": "replace 1 with motif size. For example, if motif is AAG, use 3",
205 "id": 6,
206 "input_connections": {
207 "input": {
208 "id": 5,
209 "output_name": "out_file1"
210 }
211 },
212 "inputs": [],
213 "name": "Filter",
214 "outputs": [
215 {
216 "name": "out_file1",
217 "type": "input"
218 }
219 ],
220 "position": {
221 "left": 746,
222 "top": 783
223 },
224 "post_job_actions": {
225 "HideDatasetActionout_file1": {
226 "action_arguments": {},
227 "action_type": "HideDatasetAction",
228 "output_name": "out_file1"
229 }
230 },
231 "tool_errors": null,
232 "tool_id": "Filter1",
233 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"abs(c7-c8)==1\\\"\", \"__page__\": 0}",
234 "tool_version": "1.1.0",
235 "type": "tool",
236 "user_outputs": []
237 },
238 "7": {
239 "annotation": "",
240 "id": 7,
241 "input_connections": {
242 "microsat_error_profile": {
243 "id": 0,
244 "output_name": "output"
245 },
246 "microsat_raw": {
247 "id": 6,
248 "output_name": "out_file1"
249 }
250 },
251 "inputs": [],
252 "name": "Evaluate the probability of the allele combination to generate read profile",
253 "outputs": [
254 {
255 "name": "microsat_corrected",
256 "type": "tabular"
257 }
258 ],
259 "position": {
260 "left": 708.5,
261 "top": 913
262 },
263 "post_job_actions": {
264 "HideDatasetActionmicrosat_corrected": {
265 "action_arguments": {},
266 "action_type": "HideDatasetAction",
267 "output_name": "microsat_corrected"
268 }
269 },
270 "tool_errors": null,
271 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/heteroprob/2.0.0",
272 "tool_state": "{\"microsat_raw\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"microsat_error_profile\": \"null\", \"expectedminorallele\": \"\\\"0.5\\\"\"}",
273 "tool_version": "2.0.0",
274 "type": "tool",
275 "user_outputs": []
276 },
277 "8": {
278 "annotation": "",
279 "id": 8,
280 "input_connections": {
281 "input": {
282 "id": 7,
283 "output_name": "microsat_corrected"
284 }
285 },
286 "inputs": [],
287 "name": "Sort",
288 "outputs": [
289 {
290 "name": "out_file1",
291 "type": "input"
292 }
293 ],
294 "position": {
295 "left": 761,
296 "top": 1133
297 },
298 "post_job_actions": {
299 "HideDatasetActionout_file1": {
300 "action_arguments": {},
301 "action_type": "HideDatasetAction",
302 "output_name": "out_file1"
303 }
304 },
305 "tool_errors": null,
306 "tool_id": "sort1",
307 "tool_state": "{\"__page__\": 0, \"style\": \"\\\"num\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"12\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[{\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 0, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}, \\\"other_style\\\": \\\"num\\\"}]\"}",
308 "tool_version": "1.0.3",
309 "type": "tool",
310 "user_outputs": []
311 },
312 "9": {
313 "annotation": "",
314 "id": 9,
315 "input_connections": {
316 "input": {
317 "id": 8,
318 "output_name": "out_file1"
319 }
320 },
321 "inputs": [],
322 "name": "Combine probability to generate read profile ",
323 "outputs": [
324 {
325 "name": "output",
326 "type": "tabular"
327 }
328 ],
329 "position": {
330 "left": 722,
331 "top": 1264
332 },
333 "post_job_actions": {},
334 "tool_errors": null,
335 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/combineproballelecom/2.0.0",
336 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
337 "tool_version": "2.0.0",
338 "type": "tool",
339 "user_outputs": []
340 }
341 }
342 }