Mercurial > repos > stemcellcommons > atac_seq_workflows

comparison ATAC-seq_-_Mouse_(mm9).ga @ 0:1b2ba1496c6a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial version
author stemcellcommons
date Mon, 14 Jan 2019 14:31:36 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:1b2ba1496c6a
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "{\n\t\"description\": \"Identify accessible chromatin regions. Reads are aligned to the mouse (mm9) reference genome.\",\n\t\"file_relationship\": {\n\t\t\"value_type\": \"LIST\",\n\t\t\"name\": \"List of Read Pairs\",\n\t\t\"file_relationship\": {\n\t\t\t\"file_relationship\": {},\n\t\t\t\"value_type\": \"PAIR\",\n\t\t\t\"name\": \"Read Pair\",\n\t\t\t\"input_files\": [{\n\t\t\t\t\t\"allowed_filetypes\": [{\n\t\t\t\t\t\t\"name\": \"FASTQ\"\n\t\t\t\t\t}],\n\t\t\t\t\t\"name\": \"Input File\",\n\t\t\t\t\t\"description\": \"Forward Reads\"\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\t\"allowed_filetypes\": [{\n\t\t\t\t\t\t\"name\": \"FASTQ\"\n\t\t\t\t\t}],\n\t\t\t\t\t\"name\": \"Input File\",\n\t\t\t\t\t\"description\": \"Reverse Reads\"\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t}\n}",
4 "format-version": "0.1",
5 "name": "ATAC-seq - Mouse (mm9)",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "content_id": null,
10 "errors": null,
11 "id": 0,
12 "input_connections": {},
13 "inputs": [],
14 "label": null,
15 "name": "Input dataset collection",
16 "outputs": [],
17 "position": {
18 "left": 256.5,
19 "top": 237
20 },
21 "tool_id": null,
22 "tool_state": "{\"collection_type\": \"paired\"}",
23 "tool_version": null,
24 "type": "data_collection_input",
25 "uuid": "5a8e8520-d4b1-4031-ac89-709b1988462c",
26 "workflow_outputs": [
27 {
28 "label": null,
29 "output_name": "output",
30 "uuid": "2037bfef-ffc2-4517-83eb-11e2f74318e1"
31 }
32 ]
33 },
34 "1": {
35 "annotation": "",
36 "content_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2",
37 "errors": null,
38 "id": 1,
39 "input_connections": {
40 "input_collection": {
41 "id": 0,
42 "output_name": "output"
43 }
44 },
45 "inputs": [
46 {
47 "description": "runtime parameter for tool Split Paired Collection",
48 "name": "input_collection"
49 }
50 ],
51 "label": null,
52 "name": "Split Paired Collection",
53 "outputs": [
54 {
55 "name": "forward_element",
56 "type": "data"
57 },
58 {
59 "name": "reverse_element",
60 "type": "data"
61 }
62 ],
63 "position": {
64 "left": 562,
65 "top": 221
66 },
67 "post_job_actions": {
68 "ChangeDatatypeActionforward_element": {
69 "action_arguments": {
70 "newtype": "fastqsanger"
71 },
72 "action_type": "ChangeDatatypeAction",
73 "output_name": "forward_element"
74 },
75 "ChangeDatatypeActionreverse_element": {
76 "action_arguments": {
77 "newtype": "fastqsanger"
78 },
79 "action_type": "ChangeDatatypeAction",
80 "output_name": "reverse_element"
81 },
82 "HideDatasetActionforward_element": {
83 "action_arguments": {},
84 "action_type": "HideDatasetAction",
85 "output_name": "forward_element"
86 },
87 "HideDatasetActionreverse_element": {
88 "action_arguments": {},
89 "action_type": "HideDatasetAction",
90 "output_name": "reverse_element"
91 }
92 },
93 "tool_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2",
94 "tool_shed_repository": {
95 "changeset_revision": "3a60513b51a2",
96 "name": "split_paired_collection",
97 "owner": "refinery-platform",
98 "tool_shed": "toolshed.g2.bx.psu.edu"
99 },
100 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_collection\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
101 "tool_version": "0.2",
102 "type": "tool",
103 "uuid": "6e6b7b1f-dcb2-4a40-8351-f706b535871f",
104 "workflow_outputs": []
105 },
106 "2": {
107 "annotation": "",
108 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
109 "errors": null,
110 "id": 2,
111 "input_connections": {
112 "singlePaired|pInput1": {
113 "id": 1,
114 "output_name": "forward_element"
115 },
116 "singlePaired|pInput2": {
117 "id": 1,
118 "output_name": "reverse_element"
119 }
120 },
121 "inputs": [
122 {
123 "description": "runtime parameter for tool Map with Bowtie for Illumina",
124 "name": "singlePaired"
125 },
126 {
127 "description": "runtime parameter for tool Map with Bowtie for Illumina",
128 "name": "singlePaired"
129 }
130 ],
131 "label": null,
132 "name": "Map with Bowtie for Illumina",
133 "outputs": [
134 {
135 "name": "output",
136 "type": "sam"
137 },
138 {
139 "name": "output_suppressed_reads_l",
140 "type": "fastq"
141 },
142 {
143 "name": "output_suppressed_reads_r",
144 "type": "fastq"
145 },
146 {
147 "name": "output_unmapped_reads_l",
148 "type": "fastq"
149 },
150 {
151 "name": "output_unmapped_reads_r",
152 "type": "fastq"
153 }
154 ],
155 "position": {
156 "left": 864,
157 "top": 328
158 },
159 "post_job_actions": {
160 "HideDatasetActionoutput": {
161 "action_arguments": {},
162 "action_type": "HideDatasetAction",
163 "output_name": "output"
164 },
165 "HideDatasetActionoutput_suppressed_reads_l": {
166 "action_arguments": {},
167 "action_type": "HideDatasetAction",
168 "output_name": "output_suppressed_reads_l"
169 },
170 "HideDatasetActionoutput_suppressed_reads_r": {
171 "action_arguments": {},
172 "action_type": "HideDatasetAction",
173 "output_name": "output_suppressed_reads_r"
174 },
175 "HideDatasetActionoutput_unmapped_reads_l": {
176 "action_arguments": {},
177 "action_type": "HideDatasetAction",
178 "output_name": "output_unmapped_reads_l"
179 },
180 "HideDatasetActionoutput_unmapped_reads_r": {
181 "action_arguments": {},
182 "action_type": "HideDatasetAction",
183 "output_name": "output_unmapped_reads_r"
184 }
185 },
186 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
187 "tool_shed_repository": {
188 "changeset_revision": "df86f29bedee",
189 "name": "bowtie_wrappers",
190 "owner": "devteam",
191 "tool_shed": "toolshed.g2.bx.psu.edu"
192 },
193 "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm9\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"pParams\\\": {\\\"pSettingsType\\\": \\\"preSet\\\", \\\"__current_case__\\\": 0}, \\\"pMaxInsert\\\": \\\"1000\\\", \\\"pInput2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"pInput1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sPaired\\\": \\\"paired\\\", \\\"__current_case__\\\": 1, \\\"pMateOrient\\\": \\\"fr\\\"}\"}",
194 "tool_version": "1.1.3",
195 "type": "tool",
196 "uuid": "ffb5227c-ebca-4750-a376-08e7c6c286be",
197 "workflow_outputs": []
198 },
199 "3": {
200 "annotation": "",
201 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0",
202 "errors": null,
203 "id": 3,
204 "input_connections": {
205 "source|input1": {
206 "id": 2,
207 "output_name": "output"
208 }
209 },
210 "inputs": [
211 {
212 "description": "runtime parameter for tool SAM-to-BAM",
213 "name": "source"
214 }
215 ],
216 "label": null,
217 "name": "SAM-to-BAM",
218 "outputs": [
219 {
220 "name": "output1",
221 "type": "bam"
222 }
223 ],
224 "position": {
225 "left": 1179,
226 "top": 401
227 },
228 "post_job_actions": {
229 "HideDatasetActionoutput1": {
230 "action_arguments": {},
231 "action_type": "HideDatasetAction",
232 "output_name": "output1"
233 }
234 },
235 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0",
236 "tool_shed_repository": {
237 "changeset_revision": "d04d9f1c6791",
238 "name": "sam_to_bam",
239 "owner": "devteam",
240 "tool_shed": "toolshed.g2.bx.psu.edu"
241 },
242 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm9\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
243 "tool_version": "2.0",
244 "type": "tool",
245 "uuid": "ed2ef69f-6c9a-4997-9877-f4807816b134",
246 "workflow_outputs": []
247 },
248 "4": {
249 "annotation": "",
250 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0",
251 "errors": null,
252 "id": 4,
253 "input_connections": {
254 "inputFile": {
255 "id": 3,
256 "output_name": "output1"
257 }
258 },
259 "inputs": [
260 {
261 "description": "runtime parameter for tool MarkDuplicates",
262 "name": "inputFile"
263 }
264 ],
265 "label": null,
266 "name": "MarkDuplicates",
267 "outputs": [
268 {
269 "name": "metrics_file",
270 "type": "txt"
271 },
272 {
273 "name": "outFile",
274 "type": "bam"
275 }
276 ],
277 "position": {
278 "left": 1429,
279 "top": 480
280 },
281 "post_job_actions": {
282 "HideDatasetActionmetrics_file": {
283 "action_arguments": {},
284 "action_type": "HideDatasetAction",
285 "output_name": "metrics_file"
286 }
287 },
288 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0",
289 "tool_shed_repository": {
290 "changeset_revision": "379fdf4c41ac",
291 "name": "picard",
292 "owner": "devteam",
293 "tool_shed": "toolshed.g2.bx.psu.edu"
294 },
295 "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"true\\\"\", \"read_name_regex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"validation_stringency\": \"\\\"LENIENT\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"true\\\"\", \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"inputFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
296 "tool_version": "1.126.0",
297 "type": "tool",
298 "uuid": "e142fddc-8c59-4b80-a1ff-c350b5108526",
299 "workflow_outputs": [
300 {
301 "label": null,
302 "output_name": "outFile",
303 "uuid": "7e1e6562-d64b-46e9-ba74-d5cb7bae6353"
304 }
305 ]
306 },
307 "5": {
308 "annotation": "",
309 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0",
310 "errors": null,
311 "id": 5,
312 "input_connections": {
313 "input_treatment_file": {
314 "id": 4,
315 "output_name": "outFile"
316 }
317 },
318 "inputs": [
319 {
320 "description": "runtime parameter for tool MACS2 callpeak",
321 "name": "input_control_file"
322 },
323 {
324 "description": "runtime parameter for tool MACS2 callpeak",
325 "name": "input_treatment_file"
326 }
327 ],
328 "label": null,
329 "name": "MACS2 callpeak",
330 "outputs": [
331 {
332 "name": "output_tabular",
333 "type": "tabular"
334 },
335 {
336 "name": "output_broadpeaks",
337 "type": "bed"
338 },
339 {
340 "name": "output_gappedpeaks",
341 "type": "bed"
342 },
343 {
344 "name": "output_narrowpeaks",
345 "type": "bed"
346 },
347 {
348 "name": "output_summits",
349 "type": "bed"
350 },
351 {
352 "name": "output_plot",
353 "type": "pdf"
354 },
355 {
356 "name": "output_treat_pileup",
357 "type": "bedgraph"
358 },
359 {
360 "name": "output_control_lambda",
361 "type": "bedgraph"
362 },
363 {
364 "name": "output_extra_files",
365 "type": "html"
366 }
367 ],
368 "position": {
369 "left": 1793.5,
370 "top": 597
371 },
372 "post_job_actions": {
373 "HideDatasetActionoutput_broadpeaks": {
374 "action_arguments": {},
375 "action_type": "HideDatasetAction",
376 "output_name": "output_broadpeaks"
377 },
378 "HideDatasetActionoutput_control_lambda": {
379 "action_arguments": {},
380 "action_type": "HideDatasetAction",
381 "output_name": "output_control_lambda"
382 },
383 "HideDatasetActionoutput_extra_files": {
384 "action_arguments": {},
385 "action_type": "HideDatasetAction",
386 "output_name": "output_extra_files"
387 },
388 "HideDatasetActionoutput_gappedpeaks": {
389 "action_arguments": {},
390 "action_type": "HideDatasetAction",
391 "output_name": "output_gappedpeaks"
392 },
393 "HideDatasetActionoutput_plot": {
394 "action_arguments": {},
395 "action_type": "HideDatasetAction",
396 "output_name": "output_plot"
397 },
398 "HideDatasetActionoutput_treat_pileup": {
399 "action_arguments": {},
400 "action_type": "HideDatasetAction",
401 "output_name": "output_treat_pileup"
402 }
403 },
404 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0",
405 "tool_shed_repository": {
406 "changeset_revision": "56e104999978",
407 "name": "macs2",
408 "owner": "iuc",
409 "tool_shed": "toolshed.g2.bx.psu.edu"
410 },
411 "tool_state": "{\"__page__\": null, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2150570000\\\", \\\"__current_case__\\\": 1}\", \"bampe\": \"\\\"true\\\"\", \"input_control_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"band_width\": \"\\\"300\\\"\", \"cutoff_options\": \"{\\\"cutoff_options_selector\\\": \\\"qvalue\\\", \\\"qvalue\\\": \\\"0.05\\\", \\\"__current_case__\\\": 1}\", \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"on\\\", \\\"ratio\\\": \\\"1.0\\\", \\\"to_large\\\": \\\"false\\\", \\\"slocal\\\": \\\"1000\\\", \\\"broad_options\\\": {\\\"broad_options_selector\\\": \\\"nobroad\\\", \\\"call_summits\\\": \\\"false\\\", \\\"__current_case__\\\": 1}, \\\"nolambda\\\": \\\"false\\\", \\\"llocal\\\": \\\"10000\\\", \\\"keep_dup_options\\\": {\\\"__current_case__\\\": 2, \\\"keep_dup_options_selector\\\": \\\"all\\\"}, \\\"__current_case__\\\": 0}\", \"input_treatment_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 0}\", \"outputs\": \"[\\\"peaks_tabular\\\", \\\"summits\\\", \\\"bdg\\\"]\"}",
412 "tool_version": "2.1.0.20151222.0",
413 "type": "tool",
414 "uuid": "f58a8811-f8e3-4e91-a8b9-4c635e7d00c5",
415 "workflow_outputs": [
416 {
417 "label": null,
418 "output_name": "output_tabular",
419 "uuid": "29b6c2d4-6f1a-48d2-82a3-b0d45c186bda"
420 },
421 {
422 "label": null,
423 "output_name": "output_summits",
424 "uuid": "26d6760f-5f82-4d24-a4fa-0294c37290ef"
425 },
426 {
427 "label": null,
428 "output_name": "output_narrowpeaks",
429 "uuid": "b6445346-e10b-4deb-a7e8-b8df81c73796"
430 }
431 ]
432 }
433 },
434 "uuid": "beaac1a6-7095-4c93-887c-1238cd41186e"
435 }