|
8
|
1 {
|
|
|
2 "a_galaxy_workflow": "true",
|
|
|
3 "annotation": "{\n\t\"description\": \"Identify enriched regions (peaks) in ChIP-seq data. Reads are aligned to the zebrafish (danRer7) reference genome.\",\n\t\"file_relationship\": {\n\t\t\"value_type\": \"LIST\",\n\t\t\"name\": \"List of FASTQ Pairs\",\n\t\t\"file_relationship\": {\n\t\t\t\"file_relationship\": {},\n\t\t\t\"value_type\": \"PAIR\",\n\t\t\t\"name\": \"Paired FASTQ files\",\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\": \"Treatment FASTQ\",\n\t\t\t\t\t\"description\": \"Treatment FASTQ\"\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\": \"Control FASTQ\",\n\t\t\t\t\t\"description\": \"Control FASTQ\"\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t}\n}",
|
|
|
4 "format-version": "0.1",
|
|
|
5 "name": "ChIP-seq Peak Calling - Zebrafish",
|
|
|
6 "steps": {
|
|
|
7 "0": {
|
|
|
8 "annotation": "",
|
|
|
9 "content_id": null,
|
|
|
10 "id": 0,
|
|
|
11 "input_connections": {},
|
|
|
12 "inputs": [
|
|
|
13 {
|
|
|
14 "description": "",
|
|
|
15 "name": "Input Dataset Collection"
|
|
|
16 }
|
|
|
17 ],
|
|
|
18 "label": null,
|
|
|
19 "name": "Input dataset collection",
|
|
|
20 "outputs": [],
|
|
|
21 "position": {
|
|
|
22 "left": 227,
|
|
|
23 "top": 404.5
|
|
|
24 },
|
|
|
25 "tool_errors": null,
|
|
|
26 "tool_id": null,
|
|
|
27 "tool_state": "{\"collection_type\": \"paired\", \"name\": \"Input Dataset Collection\"}",
|
|
|
28 "tool_version": null,
|
|
|
29 "type": "data_collection_input",
|
|
|
30 "uuid": "69e8d98a-a949-4cc1-bbb7-99c434e6bdd0",
|
|
|
31 "workflow_outputs": [
|
|
|
32 {
|
|
|
33 "label": null,
|
|
|
34 "output_name": "output",
|
|
|
35 "uuid": "5116f669-b430-4381-922a-89142af20c13"
|
|
|
36 }
|
|
|
37 ]
|
|
|
38 },
|
|
|
39 "1": {
|
|
|
40 "annotation": "",
|
|
|
41 "content_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2",
|
|
|
42 "id": 1,
|
|
|
43 "input_connections": {
|
|
|
44 "input_collection": {
|
|
|
45 "id": 0,
|
|
|
46 "output_name": "output"
|
|
|
47 }
|
|
|
48 },
|
|
|
49 "inputs": [],
|
|
|
50 "label": null,
|
|
|
51 "name": "Split Paired Collection",
|
|
|
52 "outputs": [
|
|
|
53 {
|
|
|
54 "name": "forward_element",
|
|
|
55 "type": "data"
|
|
|
56 },
|
|
|
57 {
|
|
|
58 "name": "reverse_element",
|
|
|
59 "type": "data"
|
|
|
60 }
|
|
|
61 ],
|
|
|
62 "position": {
|
|
|
63 "left": 551.5,
|
|
|
64 "top": 386.5
|
|
|
65 },
|
|
|
66 "post_job_actions": {
|
|
|
67 "ChangeDatatypeActionforward_element": {
|
|
|
68 "action_arguments": {
|
|
|
69 "newtype": "fastqsanger"
|
|
|
70 },
|
|
|
71 "action_type": "ChangeDatatypeAction",
|
|
|
72 "output_name": "forward_element"
|
|
|
73 },
|
|
|
74 "ChangeDatatypeActionreverse_element": {
|
|
|
75 "action_arguments": {
|
|
|
76 "newtype": "fastqsanger"
|
|
|
77 },
|
|
|
78 "action_type": "ChangeDatatypeAction",
|
|
|
79 "output_name": "reverse_element"
|
|
|
80 },
|
|
|
81 "HideDatasetActionforward_element": {
|
|
|
82 "action_arguments": {},
|
|
|
83 "action_type": "HideDatasetAction",
|
|
|
84 "output_name": "forward_element"
|
|
|
85 },
|
|
|
86 "HideDatasetActionreverse_element": {
|
|
|
87 "action_arguments": {},
|
|
|
88 "action_type": "HideDatasetAction",
|
|
|
89 "output_name": "reverse_element"
|
|
|
90 }
|
|
|
91 },
|
|
|
92 "tool_errors": null,
|
|
|
93 "tool_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2",
|
|
|
94 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_collection\": \"null\"}",
|
|
|
95 "tool_version": "0.2",
|
|
|
96 "type": "tool",
|
|
|
97 "uuid": "6c3e4f5d-d6f5-439f-8d16-c7b6ca5075de",
|
|
|
98 "workflow_outputs": []
|
|
|
99 },
|
|
|
100 "2": {
|
|
|
101 "annotation": "",
|
|
|
102 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
|
|
|
103 "id": 2,
|
|
|
104 "input_connections": {
|
|
|
105 "input_file": {
|
|
|
106 "id": 1,
|
|
|
107 "output_name": "forward_element"
|
|
|
108 }
|
|
|
109 },
|
|
|
110 "inputs": [],
|
|
|
111 "label": null,
|
|
|
112 "name": "FASTQ Parallel Groomer",
|
|
|
113 "outputs": [
|
|
|
114 {
|
|
|
115 "name": "output_file",
|
|
|
116 "type": "fastqsanger"
|
|
|
117 }
|
|
|
118 ],
|
|
|
119 "position": {
|
|
|
120 "left": 861.5,
|
|
|
121 "top": 341.265625
|
|
|
122 },
|
|
|
123 "post_job_actions": {
|
|
|
124 "HideDatasetActionoutput_file": {
|
|
|
125 "action_arguments": {},
|
|
|
126 "action_type": "HideDatasetAction",
|
|
|
127 "output_name": "output_file"
|
|
|
128 }
|
|
|
129 },
|
|
|
130 "tool_errors": null,
|
|
|
131 "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
|
|
|
132 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"options_type_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1, \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"null\"}",
|
|
|
133 "tool_version": "0.3.1",
|
|
|
134 "type": "tool",
|
|
|
135 "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f",
|
|
|
136 "workflow_outputs": []
|
|
|
137 },
|
|
|
138 "3": {
|
|
|
139 "annotation": "",
|
|
|
140 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
|
|
|
141 "id": 3,
|
|
|
142 "input_connections": {
|
|
|
143 "input_file": {
|
|
|
144 "id": 1,
|
|
|
145 "output_name": "reverse_element"
|
|
|
146 }
|
|
|
147 },
|
|
|
148 "inputs": [],
|
|
|
149 "label": null,
|
|
|
150 "name": "FASTQ Parallel Groomer",
|
|
|
151 "outputs": [
|
|
|
152 {
|
|
|
153 "name": "output_file",
|
|
|
154 "type": "fastqsanger"
|
|
|
155 }
|
|
|
156 ],
|
|
|
157 "position": {
|
|
|
158 "left": 862.5,
|
|
|
159 "top": 493.265625
|
|
|
160 },
|
|
|
161 "post_job_actions": {
|
|
|
162 "HideDatasetActionoutput_file": {
|
|
|
163 "action_arguments": {},
|
|
|
164 "action_type": "HideDatasetAction",
|
|
|
165 "output_name": "output_file"
|
|
|
166 }
|
|
|
167 },
|
|
|
168 "tool_errors": null,
|
|
|
169 "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
|
|
|
170 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"options_type_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1, \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"null\"}",
|
|
|
171 "tool_version": "0.3.1",
|
|
|
172 "type": "tool",
|
|
|
173 "uuid": "259e1093-ff1c-4f65-8432-97d5124af250",
|
|
|
174 "workflow_outputs": []
|
|
|
175 },
|
|
|
176 "4": {
|
|
|
177 "annotation": "",
|
|
|
178 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
|
|
|
179 "id": 4,
|
|
|
180 "input_connections": {
|
|
|
181 "singlePaired|sInput1": {
|
|
|
182 "id": 2,
|
|
|
183 "output_name": "output_file"
|
|
|
184 }
|
|
|
185 },
|
|
|
186 "inputs": [],
|
|
|
187 "label": null,
|
|
|
188 "name": "Map with Bowtie for Illumina",
|
|
|
189 "outputs": [
|
|
|
190 {
|
|
|
191 "name": "output",
|
|
|
192 "type": "sam"
|
|
|
193 },
|
|
|
194 {
|
|
|
195 "name": "output_suppressed_reads_l",
|
|
|
196 "type": "fastq"
|
|
|
197 },
|
|
|
198 {
|
|
|
199 "name": "output_suppressed_reads_r",
|
|
|
200 "type": "fastq"
|
|
|
201 },
|
|
|
202 {
|
|
|
203 "name": "output_unmapped_reads_l",
|
|
|
204 "type": "fastq"
|
|
|
205 },
|
|
|
206 {
|
|
|
207 "name": "output_unmapped_reads_r",
|
|
|
208 "type": "fastq"
|
|
|
209 }
|
|
|
210 ],
|
|
|
211 "position": {
|
|
|
212 "left": 1195,
|
|
|
213 "top": 272.265625
|
|
|
214 },
|
|
|
215 "post_job_actions": {
|
|
|
216 "HideDatasetActionoutput": {
|
|
|
217 "action_arguments": {},
|
|
|
218 "action_type": "HideDatasetAction",
|
|
|
219 "output_name": "output"
|
|
|
220 },
|
|
|
221 "HideDatasetActionoutput_suppressed_reads_l": {
|
|
|
222 "action_arguments": {},
|
|
|
223 "action_type": "HideDatasetAction",
|
|
|
224 "output_name": "output_suppressed_reads_l"
|
|
|
225 },
|
|
|
226 "HideDatasetActionoutput_suppressed_reads_r": {
|
|
|
227 "action_arguments": {},
|
|
|
228 "action_type": "HideDatasetAction",
|
|
|
229 "output_name": "output_suppressed_reads_r"
|
|
|
230 },
|
|
|
231 "HideDatasetActionoutput_unmapped_reads_l": {
|
|
|
232 "action_arguments": {},
|
|
|
233 "action_type": "HideDatasetAction",
|
|
|
234 "output_name": "output_unmapped_reads_l"
|
|
|
235 },
|
|
|
236 "HideDatasetActionoutput_unmapped_reads_r": {
|
|
|
237 "action_arguments": {},
|
|
|
238 "action_type": "HideDatasetAction",
|
|
|
239 "output_name": "output_unmapped_reads_r"
|
|
|
240 }
|
|
|
241 },
|
|
|
242 "tool_errors": null,
|
|
|
243 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
|
|
|
244 "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"danRer7\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"False\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"False\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}",
|
|
|
245 "tool_version": "1.1.3",
|
|
|
246 "type": "tool",
|
|
|
247 "uuid": "cd8dda4a-0a66-415c-98f0-0d6361a1abb0",
|
|
|
248 "workflow_outputs": []
|
|
|
249 },
|
|
|
250 "5": {
|
|
|
251 "annotation": "",
|
|
|
252 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
|
|
|
253 "id": 5,
|
|
|
254 "input_connections": {
|
|
|
255 "singlePaired|sInput1": {
|
|
|
256 "id": 3,
|
|
|
257 "output_name": "output_file"
|
|
|
258 }
|
|
|
259 },
|
|
|
260 "inputs": [],
|
|
|
261 "label": null,
|
|
|
262 "name": "Map with Bowtie for Illumina",
|
|
|
263 "outputs": [
|
|
|
264 {
|
|
|
265 "name": "output",
|
|
|
266 "type": "sam"
|
|
|
267 },
|
|
|
268 {
|
|
|
269 "name": "output_suppressed_reads_l",
|
|
|
270 "type": "fastq"
|
|
|
271 },
|
|
|
272 {
|
|
|
273 "name": "output_suppressed_reads_r",
|
|
|
274 "type": "fastq"
|
|
|
275 },
|
|
|
276 {
|
|
|
277 "name": "output_unmapped_reads_l",
|
|
|
278 "type": "fastq"
|
|
|
279 },
|
|
|
280 {
|
|
|
281 "name": "output_unmapped_reads_r",
|
|
|
282 "type": "fastq"
|
|
|
283 }
|
|
|
284 ],
|
|
|
285 "position": {
|
|
|
286 "left": 1199,
|
|
|
287 "top": 492.265625
|
|
|
288 },
|
|
|
289 "post_job_actions": {
|
|
|
290 "HideDatasetActionoutput": {
|
|
|
291 "action_arguments": {},
|
|
|
292 "action_type": "HideDatasetAction",
|
|
|
293 "output_name": "output"
|
|
|
294 },
|
|
|
295 "HideDatasetActionoutput_suppressed_reads_l": {
|
|
|
296 "action_arguments": {},
|
|
|
297 "action_type": "HideDatasetAction",
|
|
|
298 "output_name": "output_suppressed_reads_l"
|
|
|
299 },
|
|
|
300 "HideDatasetActionoutput_suppressed_reads_r": {
|
|
|
301 "action_arguments": {},
|
|
|
302 "action_type": "HideDatasetAction",
|
|
|
303 "output_name": "output_suppressed_reads_r"
|
|
|
304 },
|
|
|
305 "HideDatasetActionoutput_unmapped_reads_l": {
|
|
|
306 "action_arguments": {},
|
|
|
307 "action_type": "HideDatasetAction",
|
|
|
308 "output_name": "output_unmapped_reads_l"
|
|
|
309 },
|
|
|
310 "HideDatasetActionoutput_unmapped_reads_r": {
|
|
|
311 "action_arguments": {},
|
|
|
312 "action_type": "HideDatasetAction",
|
|
|
313 "output_name": "output_unmapped_reads_r"
|
|
|
314 }
|
|
|
315 },
|
|
|
316 "tool_errors": null,
|
|
|
317 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
|
|
|
318 "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"danRer7\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"False\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"False\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}",
|
|
|
319 "tool_version": "1.1.3",
|
|
|
320 "type": "tool",
|
|
|
321 "uuid": "a09286be-e5ba-45fb-be1f-585fe79cf677",
|
|
|
322 "workflow_outputs": []
|
|
|
323 },
|
|
|
324 "6": {
|
|
|
325 "annotation": "",
|
|
|
326 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1",
|
|
|
327 "id": 6,
|
|
|
328 "input_connections": {
|
|
|
329 "source|input1": {
|
|
|
330 "id": 4,
|
|
|
331 "output_name": "output"
|
|
|
332 }
|
|
|
333 },
|
|
|
334 "inputs": [],
|
|
|
335 "label": null,
|
|
|
336 "name": "SAM-to-BAM",
|
|
|
337 "outputs": [
|
|
|
338 {
|
|
|
339 "name": "output1",
|
|
|
340 "type": "bam"
|
|
|
341 }
|
|
|
342 ],
|
|
|
343 "position": {
|
|
|
344 "left": 1510,
|
|
|
345 "top": 376.265625
|
|
|
346 },
|
|
|
347 "post_job_actions": {
|
|
|
348 "HideDatasetActionoutput1": {
|
|
|
349 "action_arguments": {},
|
|
|
350 "action_type": "HideDatasetAction",
|
|
|
351 "output_name": "output1"
|
|
|
352 }
|
|
|
353 },
|
|
|
354 "tool_errors": null,
|
|
|
355 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1",
|
|
|
356 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"danRer7full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
|
357 "tool_version": "2.1",
|
|
|
358 "type": "tool",
|
|
|
359 "uuid": "03872d2a-dde5-4152-a256-04cddf41fec0",
|
|
|
360 "workflow_outputs": []
|
|
|
361 },
|
|
|
362 "7": {
|
|
|
363 "annotation": "",
|
|
|
364 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1",
|
|
|
365 "id": 7,
|
|
|
366 "input_connections": {
|
|
|
367 "source|input1": {
|
|
|
368 "id": 5,
|
|
|
369 "output_name": "output"
|
|
|
370 }
|
|
|
371 },
|
|
|
372 "inputs": [],
|
|
|
373 "label": null,
|
|
|
374 "name": "SAM-to-BAM",
|
|
|
375 "outputs": [
|
|
|
376 {
|
|
|
377 "name": "output1",
|
|
|
378 "type": "bam"
|
|
|
379 }
|
|
|
380 ],
|
|
|
381 "position": {
|
|
|
382 "left": 1511,
|
|
|
383 "top": 533.265625
|
|
|
384 },
|
|
|
385 "post_job_actions": {
|
|
|
386 "HideDatasetActionoutput1": {
|
|
|
387 "action_arguments": {},
|
|
|
388 "action_type": "HideDatasetAction",
|
|
|
389 "output_name": "output1"
|
|
|
390 }
|
|
|
391 },
|
|
|
392 "tool_errors": null,
|
|
|
393 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1",
|
|
|
394 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"danRer7full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
|
395 "tool_version": "2.1",
|
|
|
396 "type": "tool",
|
|
|
397 "uuid": "1a747633-c084-433c-8ca5-1f1196e3791f",
|
|
|
398 "workflow_outputs": []
|
|
|
399 },
|
|
|
400 "8": {
|
|
|
401 "annotation": "{\"output_tabular\": {\"name\": \"MACS2_bed\", \"description\": \"\", \"type\": \"tabular\"}, \"output_plot\": {\"name\": \"MACS2_plot\", \"description\": \"\", \"type\": \"pdf\"}}",
|
|
|
402 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0",
|
|
|
403 "id": 8,
|
|
|
404 "input_connections": {
|
|
|
405 "input_control_file": {
|
|
|
406 "id": 7,
|
|
|
407 "output_name": "output1"
|
|
|
408 },
|
|
|
409 "input_treatment_file": {
|
|
|
410 "id": 6,
|
|
|
411 "output_name": "output1"
|
|
|
412 }
|
|
|
413 },
|
|
|
414 "inputs": [],
|
|
|
415 "label": null,
|
|
|
416 "name": "MACS2 callpeak",
|
|
|
417 "outputs": [
|
|
|
418 {
|
|
|
419 "name": "output_tabular",
|
|
|
420 "type": "tabular"
|
|
|
421 },
|
|
|
422 {
|
|
|
423 "name": "output_broadpeaks",
|
|
|
424 "type": "bed"
|
|
|
425 },
|
|
|
426 {
|
|
|
427 "name": "output_gappedpeaks",
|
|
|
428 "type": "bed"
|
|
|
429 },
|
|
|
430 {
|
|
|
431 "name": "output_narrowpeaks",
|
|
|
432 "type": "bed"
|
|
|
433 },
|
|
|
434 {
|
|
|
435 "name": "output_summits",
|
|
|
436 "type": "bed"
|
|
|
437 },
|
|
|
438 {
|
|
|
439 "name": "output_plot",
|
|
|
440 "type": "pdf"
|
|
|
441 },
|
|
|
442 {
|
|
|
443 "name": "output_treat_pileup",
|
|
|
444 "type": "bedgraph"
|
|
|
445 },
|
|
|
446 {
|
|
|
447 "name": "output_control_lambda",
|
|
|
448 "type": "bedgraph"
|
|
|
449 },
|
|
|
450 {
|
|
|
451 "name": "output_extra_files",
|
|
|
452 "type": "html"
|
|
|
453 }
|
|
|
454 ],
|
|
|
455 "position": {
|
|
|
456 "left": 1750,
|
|
|
457 "top": 358.5
|
|
|
458 },
|
|
|
459 "post_job_actions": {
|
|
|
460 "HideDatasetActionoutput_broadpeaks": {
|
|
|
461 "action_arguments": {},
|
|
|
462 "action_type": "HideDatasetAction",
|
|
|
463 "output_name": "output_broadpeaks"
|
|
|
464 },
|
|
|
465 "HideDatasetActionoutput_control_lambda": {
|
|
|
466 "action_arguments": {},
|
|
|
467 "action_type": "HideDatasetAction",
|
|
|
468 "output_name": "output_control_lambda"
|
|
|
469 },
|
|
|
470 "HideDatasetActionoutput_extra_files": {
|
|
|
471 "action_arguments": {},
|
|
|
472 "action_type": "HideDatasetAction",
|
|
|
473 "output_name": "output_extra_files"
|
|
|
474 },
|
|
|
475 "HideDatasetActionoutput_gappedpeaks": {
|
|
|
476 "action_arguments": {},
|
|
|
477 "action_type": "HideDatasetAction",
|
|
|
478 "output_name": "output_gappedpeaks"
|
|
|
479 },
|
|
|
480 "HideDatasetActionoutput_narrowpeaks": {
|
|
|
481 "action_arguments": {},
|
|
|
482 "action_type": "HideDatasetAction",
|
|
|
483 "output_name": "output_narrowpeaks"
|
|
|
484 },
|
|
|
485 "HideDatasetActionoutput_summits": {
|
|
|
486 "action_arguments": {},
|
|
|
487 "action_type": "HideDatasetAction",
|
|
|
488 "output_name": "output_summits"
|
|
|
489 },
|
|
|
490 "HideDatasetActionoutput_tabular": {
|
|
|
491 "action_arguments": {},
|
|
|
492 "action_type": "HideDatasetAction",
|
|
|
493 "output_name": "output_tabular"
|
|
|
494 },
|
|
|
495 "HideDatasetActionoutput_treat_pileup": {
|
|
|
496 "action_arguments": {},
|
|
|
497 "action_type": "HideDatasetAction",
|
|
|
498 "output_name": "output_treat_pileup"
|
|
|
499 }
|
|
|
500 },
|
|
|
501 "tool_errors": null,
|
|
|
502 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0",
|
|
|
503 "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"gsize\\\": \\\"1400000000\\\", \\\"effective_genome_size_options_selector\\\": \\\"user_defined\\\", \\\"__current_case__\\\": 4}\", \"bampe\": \"\\\"False\\\"\", \"input_control_file\": \"null\", \"__rerun_remap_job_id__\": null, \"outputs\": \"[\\\"peaks_tabular\\\", \\\"bdg\\\", \\\"pdf\\\"]\", \"cutoff_options\": \"{\\\"cutoff_options_selector\\\": \\\"qvalue\\\", \\\"qvalue\\\": \\\"0.05\\\", \\\"__current_case__\\\": 1}\", \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"off\\\", \\\"__current_case__\\\": 1}\", \"input_treatment_file\": \"null\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 0}\", \"band_width\": \"\\\"300\\\"\"}",
|
|
|
504 "tool_version": "2.1.0.20151222.0",
|
|
|
505 "type": "tool",
|
|
|
506 "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7",
|
|
|
507 "workflow_outputs": [
|
|
|
508 {
|
|
|
509 "label": null,
|
|
|
510 "output_name": "output_plot",
|
|
|
511 "uuid": "32ac3a7b-5509-45fe-a69e-abfd2b33f0be"
|
|
|
512 }
|
|
|
513 ]
|
|
|
514 },
|
|
|
515 "9": {
|
|
|
516 "annotation": "",
|
|
|
517 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0",
|
|
|
518 "id": 9,
|
|
|
519 "input_connections": {
|
|
|
520 "infile_control": {
|
|
|
521 "id": 8,
|
|
|
522 "output_name": "output_control_lambda"
|
|
|
523 },
|
|
|
524 "infile_treatment": {
|
|
|
525 "id": 8,
|
|
|
526 "output_name": "output_treat_pileup"
|
|
|
527 }
|
|
|
528 },
|
|
|
529 "inputs": [],
|
|
|
530 "label": null,
|
|
|
531 "name": "MACS2 bdgcmp",
|
|
|
532 "outputs": [
|
|
|
533 {
|
|
|
534 "name": "outfile",
|
|
|
535 "type": "bedgraph"
|
|
|
536 }
|
|
|
537 ],
|
|
|
538 "position": {
|
|
|
539 "left": 2087.5,
|
|
|
540 "top": 426.5
|
|
|
541 },
|
|
|
542 "post_job_actions": {},
|
|
|
543 "tool_errors": null,
|
|
|
544 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0",
|
|
|
545 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"null\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"null\"}",
|
|
|
546 "tool_version": "2.1.0.20151222.0",
|
|
|
547 "type": "tool",
|
|
|
548 "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0",
|
|
|
549 "workflow_outputs": [
|
|
|
550 {
|
|
|
551 "label": null,
|
|
|
552 "output_name": "outfile",
|
|
|
553 "uuid": "6b9699e0-5597-4810-9e3c-1f81149ea132"
|
|
|
554 }
|
|
|
555 ]
|
|
|
556 },
|
|
|
557 "10": {
|
|
|
558 "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}",
|
|
|
559 "content_id": "wig_to_bigWig",
|
|
|
560 "id": 10,
|
|
|
561 "input_connections": {
|
|
|
562 "input1": {
|
|
|
563 "id": 9,
|
|
|
564 "output_name": "outfile"
|
|
|
565 }
|
|
|
566 },
|
|
|
567 "inputs": [],
|
|
|
568 "label": null,
|
|
|
569 "name": "Wig/BedGraph-to-bigWig",
|
|
|
570 "outputs": [
|
|
|
571 {
|
|
|
572 "name": "out_file1",
|
|
|
573 "type": "bigwig"
|
|
|
574 }
|
|
|
575 ],
|
|
|
576 "position": {
|
|
|
577 "left": 2292.546875,
|
|
|
578 "top": 447.71875
|
|
|
579 },
|
|
|
580 "post_job_actions": {},
|
|
|
581 "tool_errors": null,
|
|
|
582 "tool_id": "wig_to_bigWig",
|
|
|
583 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}",
|
|
|
584 "tool_version": "1.1.0",
|
|
|
585 "type": "tool",
|
|
|
586 "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8",
|
|
|
587 "workflow_outputs": [
|
|
|
588 {
|
|
|
589 "label": null,
|
|
|
590 "output_name": "out_file1",
|
|
|
591 "uuid": "8e824df2-af08-4fa7-bba5-221044f10c1b"
|
|
|
592 }
|
|
|
593 ]
|
|
|
594 }
|
|
|
595 },
|
|
|
596 "uuid": "bf6866e8-1ed1-4684-8dbd-fc8744257dcb"
|
|
|
597 } |
