|
0
|
1 {
|
|
|
2 "a_galaxy_workflow": "true",
|
|
|
3 "annotation": "{\n\t\"description\": \"Identify accessible chromatin regions. Reads are aligned to the mouse (mm10) 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",
|
|
|
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": 248
|
|
|
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": 232
|
|
|
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": 339
|
|
|
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\\\": \\\"mm10\\\", \\\"__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": 412
|
|
|
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\\\": \\\"mm10\\\", \\\"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": 491
|
|
|
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": 608
|
|
|
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": "0e81618b-20e0-49a5-8982-42690f42e0fe"
|
|
|
435 } |
