comparison TF_ChIP-Seq_analysis_using_MACS2__mm10.ga @ 7:f9ffbe563402 draft

Update all workflows
author stemcellcommons
date Fri, 22 Jul 2016 14:41:07 -0400
parents 4bf23bc4f4e2
children
comparison
equal deleted inserted replaced
6:e6d80da34425 7:f9ffbe563402
25 "tool_errors": null, 25 "tool_errors": null,
26 "tool_id": null, 26 "tool_id": null,
27 "tool_state": "{\"name\": \"exp_file\"}", 27 "tool_state": "{\"name\": \"exp_file\"}",
28 "tool_version": null, 28 "tool_version": null,
29 "type": "data_input", 29 "type": "data_input",
30 "uuid": "77699462-04dc-4480-a351-c3ba909c94d9", 30 "uuid": "dd984d64-daac-4547-9989-9303056523d3",
31 "workflow_outputs": [] 31 "workflow_outputs": []
32 }, 32 },
33 "1": { 33 "1": {
34 "annotation": "", 34 "annotation": "",
35 "content_id": null, 35 "content_id": null,
51 "tool_errors": null, 51 "tool_errors": null,
52 "tool_id": null, 52 "tool_id": null,
53 "tool_state": "{\"name\": \"input_file\"}", 53 "tool_state": "{\"name\": \"input_file\"}",
54 "tool_version": null, 54 "tool_version": null,
55 "type": "data_input", 55 "type": "data_input",
56 "uuid": "87084ec7-ede5-4f5a-a49c-5f96c169daa7", 56 "uuid": "7a325193-5665-4aaf-9b87-c719769f9b71",
57 "workflow_outputs": [] 57 "workflow_outputs": []
58 }, 58 },
59 "2": { 59 "2": {
60 "annotation": "", 60 "annotation": "",
61 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 61 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
64 "input_file": { 64 "input_file": {
65 "id": 0, 65 "id": 0,
66 "output_name": "output" 66 "output_name": "output"
67 } 67 }
68 }, 68 },
69 "inputs": [ 69 "inputs": [],
70 {
71 "description": "runtime parameter for tool FASTQ Parallel Groomer",
72 "name": "input_file"
73 }
74 ],
75 "label": null, 70 "label": null,
76 "name": "FASTQ Parallel Groomer", 71 "name": "FASTQ Parallel Groomer",
77 "outputs": [ 72 "outputs": [
78 { 73 {
79 "name": "output_file", 74 "name": "output_file",
91 "changeset_revision": "66ca0d174cf2", 86 "changeset_revision": "66ca0d174cf2",
92 "name": "fastq_groomer_parallel", 87 "name": "fastq_groomer_parallel",
93 "owner": "kevyin", 88 "owner": "kevyin",
94 "tool_shed": "toolshed.g2.bx.psu.edu" 89 "tool_shed": "toolshed.g2.bx.psu.edu"
95 }, 90 },
96 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"__current_case__\\\": 1, \\\"options_type_selector\\\": \\\"advanced\\\", \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 91 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"__current_case__\\\": 1, \\\"options_type_selector\\\": \\\"advanced\\\", \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"null\"}",
97 "tool_version": "0.3.1", 92 "tool_version": "0.3.1",
98 "type": "tool", 93 "type": "tool",
99 "uuid": "a91fcfa1-2ad2-4d1b-af4e-8c348ca99cf4", 94 "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f",
100 "workflow_outputs": [] 95 "workflow_outputs": []
101 }, 96 },
102 "3": { 97 "3": {
103 "annotation": "", 98 "annotation": "",
104 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 99 "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1",
107 "input_file": { 102 "input_file": {
108 "id": 1, 103 "id": 1,
109 "output_name": "output" 104 "output_name": "output"
110 } 105 }
111 }, 106 },
112 "inputs": [ 107 "inputs": [],
113 {
114 "description": "runtime parameter for tool FASTQ Parallel Groomer",
115 "name": "input_file"
116 }
117 ],
118 "label": null, 108 "label": null,
119 "name": "FASTQ Parallel Groomer", 109 "name": "FASTQ Parallel Groomer",
120 "outputs": [ 110 "outputs": [
121 { 111 {
122 "name": "output_file", 112 "name": "output_file",
134 "changeset_revision": "66ca0d174cf2", 124 "changeset_revision": "66ca0d174cf2",
135 "name": "fastq_groomer_parallel", 125 "name": "fastq_groomer_parallel",
136 "owner": "kevyin", 126 "owner": "kevyin",
137 "tool_shed": "toolshed.g2.bx.psu.edu" 127 "tool_shed": "toolshed.g2.bx.psu.edu"
138 }, 128 },
139 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"__current_case__\\\": 1, \\\"options_type_selector\\\": \\\"advanced\\\", \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 129 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"__current_case__\\\": 1, \\\"options_type_selector\\\": \\\"advanced\\\", \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"null\"}",
140 "tool_version": "0.3.1", 130 "tool_version": "0.3.1",
141 "type": "tool", 131 "type": "tool",
142 "uuid": "93829f40-3abf-4aa3-8951-46b67cf86a95", 132 "uuid": "259e1093-ff1c-4f65-8432-97d5124af250",
143 "workflow_outputs": [] 133 "workflow_outputs": []
144 }, 134 },
145 "4": { 135 "4": {
146 "annotation": "", 136 "annotation": "",
147 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", 137 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
150 "singlePaired|sInput1": { 140 "singlePaired|sInput1": {
151 "id": 2, 141 "id": 2,
152 "output_name": "output_file" 142 "output_name": "output_file"
153 } 143 }
154 }, 144 },
155 "inputs": [ 145 "inputs": [],
156 {
157 "description": "runtime parameter for tool Map with Bowtie for Illumina",
158 "name": "singlePaired"
159 }
160 ],
161 "label": null, 146 "label": null,
162 "name": "Map with Bowtie for Illumina", 147 "name": "Map with Bowtie for Illumina",
163 "outputs": [ 148 "outputs": [
164 { 149 {
165 "name": "output", 150 "name": "output",
193 "changeset_revision": "df86f29bedee", 178 "changeset_revision": "df86f29bedee",
194 "name": "bowtie_wrappers", 179 "name": "bowtie_wrappers",
195 "owner": "devteam", 180 "owner": "devteam",
196 "tool_shed": "toolshed.g2.bx.psu.edu" 181 "tool_shed": "toolshed.g2.bx.psu.edu"
197 }, 182 },
198 "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm10\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"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}\"}", 183 "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm10\\\", \\\"__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}\"}",
199 "tool_version": "1.1.3", 184 "tool_version": "1.1.3",
200 "type": "tool", 185 "type": "tool",
201 "uuid": "9ec994d9-7309-4655-b3d8-cca2de8de69b", 186 "uuid": "cd8dda4a-0a66-415c-98f0-0d6361a1abb0",
202 "workflow_outputs": [] 187 "workflow_outputs": []
203 }, 188 },
204 "5": { 189 "5": {
205 "annotation": "", 190 "annotation": "",
206 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", 191 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
209 "singlePaired|sInput1": { 194 "singlePaired|sInput1": {
210 "id": 3, 195 "id": 3,
211 "output_name": "output_file" 196 "output_name": "output_file"
212 } 197 }
213 }, 198 },
214 "inputs": [ 199 "inputs": [],
215 {
216 "description": "runtime parameter for tool Map with Bowtie for Illumina",
217 "name": "singlePaired"
218 }
219 ],
220 "label": null, 200 "label": null,
221 "name": "Map with Bowtie for Illumina", 201 "name": "Map with Bowtie for Illumina",
222 "outputs": [ 202 "outputs": [
223 { 203 {
224 "name": "output", 204 "name": "output",
252 "changeset_revision": "df86f29bedee", 232 "changeset_revision": "df86f29bedee",
253 "name": "bowtie_wrappers", 233 "name": "bowtie_wrappers",
254 "owner": "devteam", 234 "owner": "devteam",
255 "tool_shed": "toolshed.g2.bx.psu.edu" 235 "tool_shed": "toolshed.g2.bx.psu.edu"
256 }, 236 },
257 "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm10\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"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}\"}", 237 "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm10\\\", \\\"__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}\"}",
258 "tool_version": "1.1.3", 238 "tool_version": "1.1.3",
259 "type": "tool", 239 "type": "tool",
260 "uuid": "20e8c743-50c8-4afa-9fda-54b0207d7e8f", 240 "uuid": "a09286be-e5ba-45fb-be1f-585fe79cf677",
261 "workflow_outputs": [] 241 "workflow_outputs": []
262 }, 242 },
263 "6": { 243 "6": {
264 "annotation": "", 244 "annotation": "",
265 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", 245 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0",
268 "source|input1": { 248 "source|input1": {
269 "id": 4, 249 "id": 4,
270 "output_name": "output" 250 "output_name": "output"
271 } 251 }
272 }, 252 },
273 "inputs": [ 253 "inputs": [],
274 {
275 "description": "runtime parameter for tool SAM-to-BAM",
276 "name": "source"
277 }
278 ],
279 "label": null, 254 "label": null,
280 "name": "SAM-to-BAM", 255 "name": "SAM-to-BAM",
281 "outputs": [ 256 "outputs": [
282 { 257 {
283 "name": "output1", 258 "name": "output1",
295 "changeset_revision": "d04d9f1c6791", 270 "changeset_revision": "d04d9f1c6791",
296 "name": "sam_to_bam", 271 "name": "sam_to_bam",
297 "owner": "devteam", 272 "owner": "devteam",
298 "tool_shed": "toolshed.g2.bx.psu.edu" 273 "tool_shed": "toolshed.g2.bx.psu.edu"
299 }, 274 },
300 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm10\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 275 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm10full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
301 "tool_version": "2.0", 276 "tool_version": "2.0",
302 "type": "tool", 277 "type": "tool",
303 "uuid": "5c875347-40cd-4522-a57a-ca380f976df4", 278 "uuid": "03872d2a-dde5-4152-a256-04cddf41fec0",
304 "workflow_outputs": [] 279 "workflow_outputs": []
305 }, 280 },
306 "7": { 281 "7": {
307 "annotation": "", 282 "annotation": "",
308 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", 283 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0",
311 "source|input1": { 286 "source|input1": {
312 "id": 5, 287 "id": 5,
313 "output_name": "output" 288 "output_name": "output"
314 } 289 }
315 }, 290 },
316 "inputs": [ 291 "inputs": [],
317 {
318 "description": "runtime parameter for tool SAM-to-BAM",
319 "name": "source"
320 }
321 ],
322 "label": null, 292 "label": null,
323 "name": "SAM-to-BAM", 293 "name": "SAM-to-BAM",
324 "outputs": [ 294 "outputs": [
325 { 295 {
326 "name": "output1", 296 "name": "output1",
338 "changeset_revision": "d04d9f1c6791", 308 "changeset_revision": "d04d9f1c6791",
339 "name": "sam_to_bam", 309 "name": "sam_to_bam",
340 "owner": "devteam", 310 "owner": "devteam",
341 "tool_shed": "toolshed.g2.bx.psu.edu" 311 "tool_shed": "toolshed.g2.bx.psu.edu"
342 }, 312 },
343 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm10\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 313 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm10full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
344 "tool_version": "2.0", 314 "tool_version": "2.0",
345 "type": "tool", 315 "type": "tool",
346 "uuid": "6f3e360c-d5b4-46bb-9a3d-e56c78651cee", 316 "uuid": "1a747633-c084-433c-8ca5-1f1196e3791f",
347 "workflow_outputs": [] 317 "workflow_outputs": []
348 }, 318 },
349 "8": { 319 "8": {
350 "annotation": "{\"output_tabular\": {\"name\": \"MACS2_bed\", \"description\": \"\", \"type\": \"tabular\"}, \"output_plot\": {\"name\": \"MACS2_plot\", \"description\": \"\", \"type\": \"pdf\"}}", 320 "annotation": "{\"output_narrowpeaks\": {\"name\": \"MACS2_bed\", \"description\": \"\", \"type\": \"bed\"}, \"output_plot\": {\"name\": \"MACS2_plot\", \"description\": \"\", \"type\": \"pdf\"}}",
351 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", 321 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0",
352 "id": 8, 322 "id": 8,
353 "input_connections": { 323 "input_connections": {
354 "input_control_file": { 324 "input_control_file": {
355 "id": 7, 325 "id": 7,
358 "input_treatment_file": { 328 "input_treatment_file": {
359 "id": 6, 329 "id": 6,
360 "output_name": "output1" 330 "output_name": "output1"
361 } 331 }
362 }, 332 },
363 "inputs": [ 333 "inputs": [],
364 {
365 "description": "runtime parameter for tool MACS2 callpeak",
366 "name": "input_control_file"
367 },
368 {
369 "description": "runtime parameter for tool MACS2 callpeak",
370 "name": "input_treatment_file"
371 }
372 ],
373 "label": null, 334 "label": null,
374 "name": "MACS2 callpeak", 335 "name": "MACS2 callpeak",
375 "outputs": [ 336 "outputs": [
376 { 337 {
377 "name": "output_tabular", 338 "name": "output_tabular",
421 "changeset_revision": "6d4babad010f", 382 "changeset_revision": "6d4babad010f",
422 "name": "macs2", 383 "name": "macs2",
423 "owner": "iuc", 384 "owner": "iuc",
424 "tool_shed": "toolshed.g2.bx.psu.edu" 385 "tool_shed": "toolshed.g2.bx.psu.edu"
425 }, 386 },
426 "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2150570000\\\", \\\"__current_case__\\\": 1}\", \"bampe\": \"\\\"false\\\"\", \"input_control_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__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\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 0}\", \"band_width\": \"\\\"300\\\"\"}", 387 "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2150570000\\\", \\\"__current_case__\\\": 1}\", \"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\\\"\"}",
427 "tool_version": "2.1.0.20151222.0", 388 "tool_version": "2.1.0.20151222.0",
428 "type": "tool", 389 "type": "tool",
429 "uuid": "bbcb3034-f9af-4b45-b877-54822312ddac", 390 "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7",
430 "workflow_outputs": [] 391 "workflow_outputs": []
431 }, 392 },
432 "9": { 393 "9": {
433 "annotation": "", 394 "annotation": "",
434 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", 395 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0",
441 "infile_treatment": { 402 "infile_treatment": {
442 "id": 8, 403 "id": 8,
443 "output_name": "output_treat_pileup" 404 "output_name": "output_treat_pileup"
444 } 405 }
445 }, 406 },
446 "inputs": [ 407 "inputs": [],
447 {
448 "description": "runtime parameter for tool MACS2 bdgcmp",
449 "name": "infile_control"
450 },
451 {
452 "description": "runtime parameter for tool MACS2 bdgcmp",
453 "name": "infile_treatment"
454 }
455 ],
456 "label": null, 408 "label": null,
457 "name": "MACS2 bdgcmp", 409 "name": "MACS2 bdgcmp",
458 "outputs": [ 410 "outputs": [
459 { 411 {
460 "name": "outfile", 412 "name": "outfile",
472 "changeset_revision": "6d4babad010f", 424 "changeset_revision": "6d4babad010f",
473 "name": "macs2", 425 "name": "macs2",
474 "owner": "iuc", 426 "owner": "iuc",
475 "tool_shed": "toolshed.g2.bx.psu.edu" 427 "tool_shed": "toolshed.g2.bx.psu.edu"
476 }, 428 },
477 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 429 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"null\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"null\"}",
478 "tool_version": "2.1.0.20151222.0", 430 "tool_version": "2.1.0.20151222.0",
479 "type": "tool", 431 "type": "tool",
480 "uuid": "21c64164-b151-4bc4-88c8-3c3a68401a41", 432 "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0",
481 "workflow_outputs": [] 433 "workflow_outputs": []
482 }, 434 },
483 "10": { 435 "10": {
484 "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}", 436 "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}",
485 "content_id": "wig_to_bigWig", 437 "content_id": "wig_to_bigWig",
488 "input1": { 440 "input1": {
489 "id": 9, 441 "id": 9,
490 "output_name": "outfile" 442 "output_name": "outfile"
491 } 443 }
492 }, 444 },
493 "inputs": [ 445 "inputs": [],
494 {
495 "description": "runtime parameter for tool Wig/BedGraph-to-bigWig",
496 "name": "input1"
497 }
498 ],
499 "label": null, 446 "label": null,
500 "name": "Wig/BedGraph-to-bigWig", 447 "name": "Wig/BedGraph-to-bigWig",
501 "outputs": [ 448 "outputs": [
502 { 449 {
503 "name": "out_file1", 450 "name": "out_file1",
509 "top": 447.71875 456 "top": 447.71875
510 }, 457 },
511 "post_job_actions": {}, 458 "post_job_actions": {},
512 "tool_errors": null, 459 "tool_errors": null,
513 "tool_id": "wig_to_bigWig", 460 "tool_id": "wig_to_bigWig",
514 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", 461 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}",
515 "tool_version": "1.1.0", 462 "tool_version": "1.1.0",
516 "type": "tool", 463 "type": "tool",
517 "uuid": "de37a72c-ebc2-4f4f-9e80-70b11d1be79a", 464 "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8",
518 "workflow_outputs": [] 465 "workflow_outputs": []
519 } 466 }
520 }, 467 },
521 "uuid": "3be7b1f8-3931-40c8-8bb1-7fffbe2826d4" 468 "uuid": "39cc71c7-4bc2-4aae-8d0b-579055f1e196"
522 } 469 }