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": [],
|
6
|
75 "name": "Generate all possible combination of STR length profile",
|
0
|
76 "outputs": [
|
|
77 {
|
|
78 "name": "output",
|
|
79 "type": "tabular"
|
|
80 }
|
|
81 ],
|
|
82 "position": {
|
6
|
83 "left": 631.5,
|
|
84 "top": 202.5
|
0
|
85 },
|
6
|
86 "post_job_actions": {
|
|
87 "HideDatasetActionoutput": {
|
|
88 "action_arguments": {},
|
|
89 "action_type": "HideDatasetAction",
|
|
90 "output_name": "output"
|
|
91 }
|
|
92 },
|
0
|
93 "tool_errors": null,
|
6
|
94 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/Profilegenerator/2.0.0",
|
0
|
95 "tool_state": "{\"error_profile\": \"null\", \"MOTIF\": \"\\\"A\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"minprob\": \"\\\"1e-08\\\"\", \"Maxdepth\": \"\\\"30\\\"\"}",
|
|
96 "tool_version": "2.0.0",
|
|
97 "type": "tool",
|
|
98 "user_outputs": []
|
|
99 },
|
|
100 "3": {
|
|
101 "annotation": "",
|
|
102 "id": 3,
|
|
103 "input_connections": {
|
|
104 "input": {
|
|
105 "id": 2,
|
|
106 "output_name": "output"
|
|
107 }
|
|
108 },
|
|
109 "inputs": [],
|
|
110 "name": "Unique",
|
|
111 "outputs": [
|
|
112 {
|
|
113 "name": "outfile",
|
|
114 "type": "input"
|
|
115 }
|
|
116 ],
|
|
117 "position": {
|
|
118 "left": 676,
|
|
119 "top": 322
|
|
120 },
|
|
121 "post_job_actions": {
|
|
122 "HideDatasetActionoutfile": {
|
|
123 "action_arguments": {},
|
|
124 "action_type": "HideDatasetAction",
|
|
125 "output_name": "outfile"
|
|
126 }
|
|
127 },
|
|
128 "tool_errors": null,
|
|
129 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
|
|
130 "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\"}",
|
|
131 "tool_version": "0.3",
|
|
132 "type": "tool",
|
|
133 "user_outputs": []
|
|
134 },
|
|
135 "4": {
|
|
136 "annotation": "",
|
|
137 "id": 4,
|
|
138 "input_connections": {
|
|
139 "microsat_error_profile": {
|
|
140 "id": 0,
|
|
141 "output_name": "output"
|
|
142 },
|
|
143 "microsat_raw": {
|
|
144 "id": 3,
|
|
145 "output_name": "outfile"
|
|
146 }
|
|
147 },
|
|
148 "inputs": [],
|
6
|
149 "name": "Correct genotype for STR errors",
|
0
|
150 "outputs": [
|
|
151 {
|
|
152 "name": "microsat_corrected",
|
|
153 "type": "tabular"
|
|
154 }
|
|
155 ],
|
|
156 "position": {
|
6
|
157 "left": 658,
|
|
158 "top": 436.5
|
0
|
159 },
|
|
160 "post_job_actions": {
|
|
161 "HideDatasetActionmicrosat_corrected": {
|
|
162 "action_arguments": {},
|
|
163 "action_type": "HideDatasetAction",
|
|
164 "output_name": "microsat_corrected"
|
|
165 }
|
|
166 },
|
|
167 "tool_errors": null,
|
6
|
168 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/GenotypeSTR/2.0.0",
|
0
|
169 "tool_state": "{\"microsat_raw\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"microsat_error_profile\": \"null\", \"expectedminorallele\": \"\\\"0.5\\\"\"}",
|
|
170 "tool_version": "2.0.0",
|
|
171 "type": "tool",
|
|
172 "user_outputs": []
|
|
173 },
|
|
174 "5": {
|
|
175 "annotation": "",
|
|
176 "id": 5,
|
|
177 "input_connections": {
|
|
178 "input": {
|
|
179 "id": 4,
|
|
180 "output_name": "microsat_corrected"
|
|
181 }
|
|
182 },
|
|
183 "inputs": [],
|
|
184 "name": "Select",
|
|
185 "outputs": [
|
|
186 {
|
|
187 "name": "out_file1",
|
|
188 "type": "input"
|
|
189 }
|
|
190 ],
|
|
191 "position": {
|
|
192 "left": 732,
|
|
193 "top": 629
|
|
194 },
|
|
195 "post_job_actions": {
|
|
196 "HideDatasetActionout_file1": {
|
|
197 "action_arguments": {},
|
|
198 "action_type": "HideDatasetAction",
|
|
199 "output_name": "out_file1"
|
|
200 }
|
|
201 },
|
|
202 "tool_errors": null,
|
|
203 "tool_id": "Grep1",
|
|
204 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"pattern\": \"\\\"hetero\\\"\"}",
|
|
205 "tool_version": "1.0.1",
|
|
206 "type": "tool",
|
|
207 "user_outputs": []
|
|
208 },
|
|
209 "6": {
|
|
210 "annotation": "replace 1 with motif size. For example, if motif is AAG, use 3",
|
|
211 "id": 6,
|
|
212 "input_connections": {
|
|
213 "input": {
|
|
214 "id": 5,
|
|
215 "output_name": "out_file1"
|
|
216 }
|
|
217 },
|
|
218 "inputs": [],
|
|
219 "name": "Filter",
|
|
220 "outputs": [
|
|
221 {
|
|
222 "name": "out_file1",
|
|
223 "type": "input"
|
|
224 }
|
|
225 ],
|
|
226 "position": {
|
|
227 "left": 746,
|
|
228 "top": 783
|
|
229 },
|
|
230 "post_job_actions": {
|
|
231 "HideDatasetActionout_file1": {
|
|
232 "action_arguments": {},
|
|
233 "action_type": "HideDatasetAction",
|
|
234 "output_name": "out_file1"
|
|
235 }
|
|
236 },
|
|
237 "tool_errors": null,
|
|
238 "tool_id": "Filter1",
|
|
239 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"abs(c7-c8)==1\\\"\", \"__page__\": 0}",
|
|
240 "tool_version": "1.1.0",
|
|
241 "type": "tool",
|
|
242 "user_outputs": []
|
|
243 },
|
|
244 "7": {
|
|
245 "annotation": "",
|
|
246 "id": 7,
|
|
247 "input_connections": {
|
|
248 "microsat_error_profile": {
|
|
249 "id": 0,
|
|
250 "output_name": "output"
|
|
251 },
|
|
252 "microsat_raw": {
|
|
253 "id": 6,
|
|
254 "output_name": "out_file1"
|
|
255 }
|
|
256 },
|
|
257 "inputs": [],
|
|
258 "name": "Evaluate the probability of the allele combination to generate read profile",
|
|
259 "outputs": [
|
|
260 {
|
|
261 "name": "microsat_corrected",
|
|
262 "type": "tabular"
|
|
263 }
|
|
264 ],
|
|
265 "position": {
|
6
|
266 "left": 720,
|
|
267 "top": 897.5
|
0
|
268 },
|
|
269 "post_job_actions": {
|
|
270 "HideDatasetActionmicrosat_corrected": {
|
|
271 "action_arguments": {},
|
|
272 "action_type": "HideDatasetAction",
|
|
273 "output_name": "microsat_corrected"
|
|
274 }
|
|
275 },
|
|
276 "tool_errors": null,
|
6
|
277 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/heteroprob/2.0.0",
|
0
|
278 "tool_state": "{\"microsat_raw\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"microsat_error_profile\": \"null\", \"expectedminorallele\": \"\\\"0.5\\\"\"}",
|
|
279 "tool_version": "2.0.0",
|
|
280 "type": "tool",
|
|
281 "user_outputs": []
|
|
282 },
|
|
283 "8": {
|
|
284 "annotation": "",
|
|
285 "id": 8,
|
|
286 "input_connections": {
|
|
287 "input": {
|
|
288 "id": 7,
|
|
289 "output_name": "microsat_corrected"
|
|
290 }
|
|
291 },
|
|
292 "inputs": [],
|
|
293 "name": "Sort",
|
|
294 "outputs": [
|
|
295 {
|
|
296 "name": "out_file1",
|
|
297 "type": "input"
|
|
298 }
|
|
299 ],
|
|
300 "position": {
|
|
301 "left": 761,
|
|
302 "top": 1133
|
|
303 },
|
|
304 "post_job_actions": {
|
|
305 "HideDatasetActionout_file1": {
|
|
306 "action_arguments": {},
|
|
307 "action_type": "HideDatasetAction",
|
|
308 "output_name": "out_file1"
|
|
309 }
|
|
310 },
|
|
311 "tool_errors": null,
|
|
312 "tool_id": "sort1",
|
|
313 "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\\\"}]\"}",
|
|
314 "tool_version": "1.0.3",
|
|
315 "type": "tool",
|
|
316 "user_outputs": []
|
|
317 },
|
|
318 "9": {
|
|
319 "annotation": "",
|
|
320 "id": 9,
|
|
321 "input_connections": {
|
|
322 "input": {
|
|
323 "id": 8,
|
|
324 "output_name": "out_file1"
|
|
325 }
|
|
326 },
|
|
327 "inputs": [],
|
6
|
328 "name": "Combine read profile probabilities ",
|
0
|
329 "outputs": [
|
|
330 {
|
|
331 "name": "output",
|
|
332 "type": "tabular"
|
|
333 }
|
|
334 ],
|
|
335 "position": {
|
6
|
336 "left": 737.5,
|
|
337 "top": 1273.5
|
0
|
338 },
|
|
339 "post_job_actions": {},
|
|
340 "tool_errors": null,
|
6
|
341 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/combineproballelecom/2.0.0",
|
0
|
342 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
343 "tool_version": "2.0.0",
|
|
344 "type": "tool",
|
|
345 "user_outputs": []
|
|
346 }
|
|
347 }
|
|
348 } |