0
|
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 } |