2
|
1 {
|
|
2 "a_galaxy_workflow": "true",
|
|
3 "annotation": "{\"refinery_type\": \"analysis\", \"refinery_relationships\": [{\"category\": \"1-1\", \"set1\": \"input_file\", \"set2\": \"exp_file\"}]}",
|
|
4 "format-version": "0.1",
|
|
5 "name": "TF ChIP-Seq analysis using MACS2: hg19",
|
|
6 "steps": {
|
|
7 "0": {
|
|
8 "annotation": "",
|
|
9 "id": 0,
|
|
10 "input_connections": {},
|
|
11 "inputs": [
|
|
12 {
|
|
13 "description": "",
|
|
14 "name": "exp_file"
|
|
15 }
|
|
16 ],
|
|
17 "name": "Input dataset",
|
|
18 "outputs": [],
|
|
19 "position": {
|
|
20 "left": 206,
|
|
21 "top": 381.265625
|
|
22 },
|
|
23 "tool_errors": null,
|
|
24 "tool_id": null,
|
|
25 "tool_state": "{\"name\": \"exp_file\"}",
|
|
26 "tool_version": null,
|
|
27 "type": "data_input",
|
|
28 "user_outputs": []
|
|
29 },
|
|
30 "1": {
|
|
31 "annotation": "",
|
|
32 "id": 1,
|
|
33 "input_connections": {},
|
|
34 "inputs": [
|
|
35 {
|
|
36 "description": "",
|
|
37 "name": "input_file"
|
|
38 }
|
|
39 ],
|
|
40 "name": "Input dataset",
|
|
41 "outputs": [],
|
|
42 "position": {
|
|
43 "left": 201,
|
|
44 "top": 516.265625
|
|
45 },
|
|
46 "tool_errors": null,
|
|
47 "tool_id": null,
|
|
48 "tool_state": "{\"name\": \"input_file\"}",
|
|
49 "tool_version": null,
|
|
50 "type": "data_input",
|
|
51 "user_outputs": []
|
|
52 },
|
|
53 "2": {
|
|
54 "annotation": "",
|
|
55 "id": 2,
|
|
56 "input_connections": {
|
|
57 "input_file": {
|
|
58 "id": 0,
|
|
59 "output_name": "output"
|
|
60 }
|
|
61 },
|
|
62 "inputs": [],
|
|
63 "name": "FASTQ Parallel Groomer",
|
|
64 "outputs": [
|
|
65 {
|
|
66 "name": "output_file",
|
|
67 "type": "fastqsanger"
|
|
68 }
|
|
69 ],
|
|
70 "position": {
|
|
71 "left": 422,
|
|
72 "top": 341.265625
|
|
73 },
|
|
74 "post_job_actions": {},
|
|
75 "tool_errors": null,
|
|
76 "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
|
|
77 "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\"}",
|
|
78 "tool_version": "0.3.1",
|
|
79 "type": "tool",
|
|
80 "user_outputs": []
|
|
81 },
|
|
82 "3": {
|
|
83 "annotation": "",
|
|
84 "id": 3,
|
|
85 "input_connections": {
|
|
86 "input_file": {
|
|
87 "id": 1,
|
|
88 "output_name": "output"
|
|
89 }
|
|
90 },
|
|
91 "inputs": [],
|
|
92 "name": "FASTQ Parallel Groomer",
|
|
93 "outputs": [
|
|
94 {
|
|
95 "name": "output_file",
|
|
96 "type": "fastqsanger"
|
|
97 }
|
|
98 ],
|
|
99 "position": {
|
|
100 "left": 423,
|
|
101 "top": 493.265625
|
|
102 },
|
|
103 "post_job_actions": {},
|
|
104 "tool_errors": null,
|
|
105 "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
|
|
106 "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\"}",
|
|
107 "tool_version": "0.3.1",
|
|
108 "type": "tool",
|
|
109 "user_outputs": []
|
|
110 },
|
|
111 "4": {
|
|
112 "annotation": "",
|
|
113 "id": 4,
|
|
114 "input_connections": {
|
|
115 "singlePaired|sInput1": {
|
|
116 "id": 2,
|
|
117 "output_name": "output_file"
|
|
118 }
|
|
119 },
|
|
120 "inputs": [],
|
|
121 "name": "Map with Bowtie for Illumina",
|
|
122 "outputs": [
|
|
123 {
|
|
124 "name": "output",
|
|
125 "type": "sam"
|
|
126 },
|
|
127 {
|
|
128 "name": "output_suppressed_reads_l",
|
|
129 "type": "fastq"
|
|
130 },
|
|
131 {
|
|
132 "name": "output_suppressed_reads_r",
|
|
133 "type": "fastq"
|
|
134 },
|
|
135 {
|
|
136 "name": "output_unmapped_reads_l",
|
|
137 "type": "fastq"
|
|
138 },
|
|
139 {
|
|
140 "name": "output_unmapped_reads_r",
|
|
141 "type": "fastq"
|
|
142 }
|
|
143 ],
|
|
144 "position": {
|
|
145 "left": 755.5,
|
|
146 "top": 272.265625
|
|
147 },
|
|
148 "post_job_actions": {},
|
|
149 "tool_errors": null,
|
|
150 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
|
|
151 "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19\\\", \\\"__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}\"}",
|
|
152 "tool_version": "1.1.3",
|
|
153 "type": "tool",
|
|
154 "user_outputs": []
|
|
155 },
|
|
156 "5": {
|
|
157 "annotation": "",
|
|
158 "id": 5,
|
|
159 "input_connections": {
|
|
160 "singlePaired|sInput1": {
|
|
161 "id": 3,
|
|
162 "output_name": "output_file"
|
|
163 }
|
|
164 },
|
|
165 "inputs": [],
|
|
166 "name": "Map with Bowtie for Illumina",
|
|
167 "outputs": [
|
|
168 {
|
|
169 "name": "output",
|
|
170 "type": "sam"
|
|
171 },
|
|
172 {
|
|
173 "name": "output_suppressed_reads_l",
|
|
174 "type": "fastq"
|
|
175 },
|
|
176 {
|
|
177 "name": "output_suppressed_reads_r",
|
|
178 "type": "fastq"
|
|
179 },
|
|
180 {
|
|
181 "name": "output_unmapped_reads_l",
|
|
182 "type": "fastq"
|
|
183 },
|
|
184 {
|
|
185 "name": "output_unmapped_reads_r",
|
|
186 "type": "fastq"
|
|
187 }
|
|
188 ],
|
|
189 "position": {
|
|
190 "left": 759.5,
|
|
191 "top": 492.265625
|
|
192 },
|
|
193 "post_job_actions": {},
|
|
194 "tool_errors": null,
|
|
195 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
|
|
196 "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19\\\", \\\"__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}\"}",
|
|
197 "tool_version": "1.1.3",
|
|
198 "type": "tool",
|
|
199 "user_outputs": []
|
|
200 },
|
|
201 "6": {
|
|
202 "annotation": "",
|
|
203 "id": 6,
|
|
204 "input_connections": {
|
|
205 "source|input1": {
|
|
206 "id": 4,
|
|
207 "output_name": "output"
|
|
208 }
|
|
209 },
|
|
210 "inputs": [],
|
|
211 "name": "SAM-to-BAM",
|
|
212 "outputs": [
|
|
213 {
|
|
214 "name": "output1",
|
|
215 "type": "bam"
|
|
216 }
|
|
217 ],
|
|
218 "position": {
|
|
219 "left": 1069.5,
|
|
220 "top": 376.265625
|
|
221 },
|
|
222 "post_job_actions": {},
|
|
223 "tool_errors": null,
|
|
224 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1",
|
|
225 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19full\\\"}, \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
226 "tool_version": "2.1",
|
|
227 "type": "tool",
|
|
228 "user_outputs": []
|
|
229 },
|
|
230 "7": {
|
|
231 "annotation": "",
|
|
232 "id": 7,
|
|
233 "input_connections": {
|
|
234 "source|input1": {
|
|
235 "id": 5,
|
|
236 "output_name": "output"
|
|
237 }
|
|
238 },
|
|
239 "inputs": [],
|
|
240 "name": "SAM-to-BAM",
|
|
241 "outputs": [
|
|
242 {
|
|
243 "name": "output1",
|
|
244 "type": "bam"
|
|
245 }
|
|
246 ],
|
|
247 "position": {
|
|
248 "left": 1071.5,
|
|
249 "top": 533.265625
|
|
250 },
|
|
251 "post_job_actions": {},
|
|
252 "tool_errors": null,
|
|
253 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1",
|
|
254 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19full\\\"}, \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
255 "tool_version": "2.1",
|
|
256 "type": "tool",
|
|
257 "user_outputs": []
|
|
258 },
|
|
259 "8": {
|
|
260 "annotation": "{\"output_tabular\": {\"name\": \"MACS2_bed\", \"description\": \"\", \"type\": \"tabular\"}, \"output_plot\": {\"name\": \"MACS2_plot\", \"description\": \"\", \"type\": \"pdf\"}}",
|
|
261 "id": 8,
|
|
262 "input_connections": {
|
|
263 "input_control_file": {
|
|
264 "id": 7,
|
|
265 "output_name": "output1"
|
|
266 },
|
|
267 "input_treatment_file": {
|
|
268 "id": 6,
|
|
269 "output_name": "output1"
|
|
270 }
|
|
271 },
|
|
272 "inputs": [],
|
|
273 "name": "MACS2 callpeak",
|
|
274 "outputs": [
|
|
275 {
|
|
276 "name": "output_tabular",
|
|
277 "type": "tabular"
|
|
278 },
|
|
279 {
|
|
280 "name": "output_broadpeaks",
|
|
281 "type": "bed"
|
|
282 },
|
|
283 {
|
|
284 "name": "output_gappedpeaks",
|
|
285 "type": "bed"
|
|
286 },
|
|
287 {
|
|
288 "name": "output_narrowpeaks",
|
|
289 "type": "bed"
|
|
290 },
|
|
291 {
|
|
292 "name": "output_summits",
|
|
293 "type": "bed"
|
|
294 },
|
|
295 {
|
|
296 "name": "output_plot",
|
|
297 "type": "pdf"
|
|
298 },
|
|
299 {
|
|
300 "name": "output_treat_pileup",
|
|
301 "type": "bedgraph"
|
|
302 },
|
|
303 {
|
|
304 "name": "output_control_lambda",
|
|
305 "type": "bedgraph"
|
|
306 },
|
|
307 {
|
|
308 "name": "output_extra_files",
|
|
309 "type": "html"
|
|
310 }
|
|
311 ],
|
|
312 "position": {
|
|
313 "left": 1310.5,
|
|
314 "top": 358.5
|
|
315 },
|
|
316 "post_job_actions": {},
|
|
317 "tool_errors": null,
|
|
318 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0",
|
|
319 "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2451960000\\\", \\\"__current_case__\\\": 0}\", \"bampe\": \"\\\"False\\\"\", \"input_control_file\": \"null\", \"__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\\\": \\\"off\\\", \\\"__current_case__\\\": 1}\", \"input_treatment_file\": \"null\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 0}\", \"outputs\": \"[\\\"peaks_tabular\\\", \\\"bdg\\\", \\\"pdf\\\"]\"}",
|
|
320 "tool_version": "2.1.0.20151222.0",
|
|
321 "type": "tool",
|
|
322 "user_outputs": []
|
|
323 },
|
|
324 "9": {
|
|
325 "annotation": "",
|
|
326 "id": 9,
|
|
327 "input_connections": {
|
|
328 "infile_control": {
|
|
329 "id": 8,
|
|
330 "output_name": "output_control_lambda"
|
|
331 },
|
|
332 "infile_treatment": {
|
|
333 "id": 8,
|
|
334 "output_name": "output_treat_pileup"
|
|
335 }
|
|
336 },
|
|
337 "inputs": [],
|
|
338 "name": "MACS2 bdgcmp",
|
|
339 "outputs": [
|
|
340 {
|
|
341 "name": "outfile",
|
|
342 "type": "bedgraph"
|
|
343 }
|
|
344 ],
|
|
345 "position": {
|
|
346 "left": 1648,
|
|
347 "top": 426.5
|
|
348 },
|
|
349 "post_job_actions": {},
|
|
350 "tool_errors": null,
|
|
351 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0",
|
|
352 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"null\", \"infile_treatment\": \"null\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\"}",
|
|
353 "tool_version": "2.1.0.20151222.0",
|
|
354 "type": "tool",
|
|
355 "user_outputs": []
|
|
356 },
|
|
357 "10": {
|
|
358 "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}",
|
|
359 "id": 10,
|
|
360 "input_connections": {
|
|
361 "input1": {
|
|
362 "id": 9,
|
|
363 "output_name": "outfile"
|
|
364 }
|
|
365 },
|
|
366 "inputs": [],
|
|
367 "name": "Wig/BedGraph-to-bigWig",
|
|
368 "outputs": [
|
|
369 {
|
|
370 "name": "out_file1",
|
|
371 "type": "bigwig"
|
|
372 }
|
|
373 ],
|
|
374 "position": {
|
|
375 "left": 1853.046875,
|
|
376 "top": 447.71875
|
|
377 },
|
|
378 "post_job_actions": {},
|
|
379 "tool_errors": null,
|
|
380 "tool_id": "wig_to_bigWig",
|
|
381 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}",
|
|
382 "tool_version": "1.1.0",
|
|
383 "type": "tool",
|
|
384 "user_outputs": []
|
|
385 }
|
|
386 }
|
|
387 } |