Mercurial > repos > stemcellcommons > chipseq_workflows
comparison ChIP-seq_Peak_Calling_-_Mouse.ga @ 8:358360fdeea9 draft
Update annotation
| author | stemcellcommons |
|---|---|
| date | Tue, 24 Oct 2017 16:48:56 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 7:f9ffbe563402 | 8:358360fdeea9 |
|---|---|
| 1 { | |
| 2 "a_galaxy_workflow": "true", | |
| 3 "annotation": "{\n\t\"description\": \"Identify enriched regions (peaks) in ChIP-seq data. 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 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 - Mouse", | |
| 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": 200, | |
| 23 "top": 395.5 | |
| 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": "356ec3d6-e4d4-442c-bbd6-84acab454f1a", | |
| 31 "workflow_outputs": [ | |
| 32 { | |
| 33 "label": null, | |
| 34 "output_name": "output", | |
| 35 "uuid": "f6218906-b7d9-45d0-8d2a-1eb96c3e9a8e" | |
| 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": 474.5, | |
| 64 "top": 376.5 | |
| 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": "0b53727d-3d55-470e-b8d4-3d4a38fbfdf5", | |
| 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": 775.5, | |
| 121 "top": 342.265625 | |
| 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": 776.5, | |
| 159 "top": 494.265625 | |
| 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": 1109, | |
| 213 "top": 273.265625 | |
| 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\\\": \\\"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}\"}", | |
| 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": 1113, | |
| 287 "top": 493.265625 | |
| 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\\\": \\\"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}\"}", | |
| 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": 1424, | |
| 345 "top": 377.265625 | |
| 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\\\": \\\"mm10full\\\", \\\"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": 1425, | |
| 383 "top": 534.265625 | |
| 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\\\": \\\"mm10full\\\", \\\"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": 1664, | |
| 457 "top": 359.5 | |
| 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\": \"{\\\"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\\\"\"}", | |
| 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": "456fea9e-c16f-4baa-af2f-e22a65cc6b7f" | |
| 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": 2001.5, | |
| 540 "top": 427.5 | |
| 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": "9b313409-0812-495c-848b-aaab5eaf05b4" | |
| 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": 2243.546875, | |
| 578 "top": 432.71875 | |
| 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": "5bbfca2d-617f-43d8-8eb9-a4d6a9a07eb8" | |
| 592 } | |
| 593 ] | |
| 594 } | |
| 595 }, | |
| 596 "uuid": "99c95324-e964-41d7-90fe-7c70d06942cf" | |
| 597 } |
