annotate ChIP-seq_Peak_Calling_-_Zebrafish.ga @ 8:358360fdeea9 draft

Update annotation
author stemcellcommons
date Tue, 24 Oct 2017 16:48:56 -0400
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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}",
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4 "format-version": "0.1",
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5 "name": "ChIP-seq Peak Calling - Zebrafish",
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parents:
diff changeset
209 }
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stemcellcommons
parents:
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210 ],
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stemcellcommons
parents:
diff changeset
211 "position": {
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diff changeset
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stemcellcommons
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diff changeset
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stemcellcommons
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diff changeset
215 "post_job_actions": {
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stemcellcommons
parents:
diff changeset
216 "HideDatasetActionoutput": {
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stemcellcommons
parents:
diff changeset
217 "action_arguments": {},
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stemcellcommons
parents:
diff changeset
218 "action_type": "HideDatasetAction",
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stemcellcommons
parents:
diff changeset
219 "output_name": "output"
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stemcellcommons
parents:
diff changeset
220 },
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stemcellcommons
parents:
diff changeset
221 "HideDatasetActionoutput_suppressed_reads_l": {
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stemcellcommons
parents:
diff changeset
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stemcellcommons
parents:
diff changeset
223 "action_type": "HideDatasetAction",
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stemcellcommons
parents:
diff changeset
224 "output_name": "output_suppressed_reads_l"
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stemcellcommons
parents:
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225 },
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stemcellcommons
parents:
diff changeset
226 "HideDatasetActionoutput_suppressed_reads_r": {
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stemcellcommons
parents:
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227 "action_arguments": {},
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stemcellcommons
parents:
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228 "action_type": "HideDatasetAction",
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stemcellcommons
parents:
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229 "output_name": "output_suppressed_reads_r"
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stemcellcommons
parents:
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230 },
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stemcellcommons
parents:
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231 "HideDatasetActionoutput_unmapped_reads_l": {
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stemcellcommons
parents:
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232 "action_arguments": {},
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stemcellcommons
parents:
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233 "action_type": "HideDatasetAction",
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stemcellcommons
parents:
diff changeset
234 "output_name": "output_unmapped_reads_l"
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stemcellcommons
parents:
diff changeset
235 },
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stemcellcommons
parents:
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236 "HideDatasetActionoutput_unmapped_reads_r": {
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stemcellcommons
parents:
diff changeset
237 "action_arguments": {},
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stemcellcommons
parents:
diff changeset
238 "action_type": "HideDatasetAction",
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stemcellcommons
parents:
diff changeset
239 "output_name": "output_unmapped_reads_r"
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stemcellcommons
parents:
diff changeset
240 }
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stemcellcommons
parents:
diff changeset
241 },
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stemcellcommons
parents:
diff changeset
242 "tool_errors": null,
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stemcellcommons
parents:
diff changeset
243 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
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stemcellcommons
parents:
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stemcellcommons
parents:
diff changeset
245 "tool_version": "1.1.3",
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stemcellcommons
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diff changeset
246 "type": "tool",
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stemcellcommons
parents:
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stemcellcommons
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stemcellcommons
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diff changeset
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stemcellcommons
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diff changeset
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stemcellcommons
parents:
diff changeset
251 "annotation": "",
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stemcellcommons
parents:
diff changeset
252 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
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stemcellcommons
parents:
diff changeset
253 "id": 5,
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stemcellcommons
parents:
diff changeset
254 "input_connections": {
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stemcellcommons
parents:
diff changeset
255 "singlePaired|sInput1": {
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stemcellcommons
parents:
diff changeset
256 "id": 3,
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stemcellcommons
parents:
diff changeset
257 "output_name": "output_file"
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stemcellcommons
parents:
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258 }
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stemcellcommons
parents:
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259 },
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stemcellcommons
parents:
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260 "inputs": [],
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stemcellcommons
parents:
diff changeset
261 "label": null,
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stemcellcommons
parents:
diff changeset
262 "name": "Map with Bowtie for Illumina",
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stemcellcommons
parents:
diff changeset
263 "outputs": [
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stemcellcommons
parents:
diff changeset
264 {
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stemcellcommons
parents:
diff changeset
265 "name": "output",
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stemcellcommons
parents:
diff changeset
266 "type": "sam"
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stemcellcommons
parents:
diff changeset
267 },
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stemcellcommons
parents:
diff changeset
268 {
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stemcellcommons
parents:
diff changeset
269 "name": "output_suppressed_reads_l",
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stemcellcommons
parents:
diff changeset
270 "type": "fastq"
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stemcellcommons
parents:
diff changeset
271 },
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stemcellcommons
parents:
diff changeset
272 {
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stemcellcommons
parents:
diff changeset
273 "name": "output_suppressed_reads_r",
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stemcellcommons
parents:
diff changeset
274 "type": "fastq"
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stemcellcommons
parents:
diff changeset
275 },
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stemcellcommons
parents:
diff changeset
276 {
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stemcellcommons
parents:
diff changeset
277 "name": "output_unmapped_reads_l",
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stemcellcommons
parents:
diff changeset
278 "type": "fastq"
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stemcellcommons
parents:
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279 },
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stemcellcommons
parents:
diff changeset
280 {
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stemcellcommons
parents:
diff changeset
281 "name": "output_unmapped_reads_r",
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stemcellcommons
parents:
diff changeset
282 "type": "fastq"
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stemcellcommons
parents:
diff changeset
283 }
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stemcellcommons
parents:
diff changeset
284 ],
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parents:
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diff changeset
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diff changeset
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stemcellcommons
parents:
diff changeset
290 "HideDatasetActionoutput": {
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stemcellcommons
parents:
diff changeset
291 "action_arguments": {},
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stemcellcommons
parents:
diff changeset
292 "action_type": "HideDatasetAction",
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stemcellcommons
parents:
diff changeset
293 "output_name": "output"
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stemcellcommons
parents:
diff changeset
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stemcellcommons
parents:
diff changeset
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stemcellcommons
parents:
diff changeset
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stemcellcommons
parents:
diff changeset
297 "action_type": "HideDatasetAction",
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stemcellcommons
parents:
diff changeset
298 "output_name": "output_suppressed_reads_l"
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stemcellcommons
parents:
diff changeset
299 },
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stemcellcommons
parents:
diff changeset
300 "HideDatasetActionoutput_suppressed_reads_r": {
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stemcellcommons
parents:
diff changeset
301 "action_arguments": {},
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stemcellcommons
parents:
diff changeset
302 "action_type": "HideDatasetAction",
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stemcellcommons
parents:
diff changeset
303 "output_name": "output_suppressed_reads_r"
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stemcellcommons
parents:
diff changeset
304 },
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stemcellcommons
parents:
diff changeset
305 "HideDatasetActionoutput_unmapped_reads_l": {
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stemcellcommons
parents:
diff changeset
306 "action_arguments": {},
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stemcellcommons
parents:
diff changeset
307 "action_type": "HideDatasetAction",
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stemcellcommons
parents:
diff changeset
308 "output_name": "output_unmapped_reads_l"
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stemcellcommons
parents:
diff changeset
309 },
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stemcellcommons
parents:
diff changeset
310 "HideDatasetActionoutput_unmapped_reads_r": {
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stemcellcommons
parents:
diff changeset
311 "action_arguments": {},
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stemcellcommons
parents:
diff changeset
312 "action_type": "HideDatasetAction",
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stemcellcommons
parents:
diff changeset
313 "output_name": "output_unmapped_reads_r"
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stemcellcommons
parents:
diff changeset
314 }
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stemcellcommons
parents:
diff changeset
315 },
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stemcellcommons
parents:
diff changeset
316 "tool_errors": null,
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stemcellcommons
parents:
diff changeset
317 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3",
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stemcellcommons
parents:
diff changeset
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stemcellcommons
parents:
diff changeset
319 "tool_version": "1.1.3",
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stemcellcommons
parents:
diff changeset
320 "type": "tool",
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stemcellcommons
parents:
diff changeset
321 "uuid": "a09286be-e5ba-45fb-be1f-585fe79cf677",
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stemcellcommons
parents:
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322 "workflow_outputs": []
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stemcellcommons
parents:
diff changeset
323 },
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stemcellcommons
parents:
diff changeset
324 "6": {
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stemcellcommons
parents:
diff changeset
325 "annotation": "",
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stemcellcommons
parents:
diff changeset
326 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1",
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stemcellcommons
parents:
diff changeset
327 "id": 6,
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stemcellcommons
parents:
diff changeset
328 "input_connections": {
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stemcellcommons
parents:
diff changeset
329 "source|input1": {
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stemcellcommons
parents:
diff changeset
330 "id": 4,
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stemcellcommons
parents:
diff changeset
331 "output_name": "output"
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stemcellcommons
parents:
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332 }
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stemcellcommons
parents:
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333 },
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stemcellcommons
parents:
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334 "inputs": [],
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stemcellcommons
parents:
diff changeset
335 "label": null,
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stemcellcommons
parents:
diff changeset
336 "name": "SAM-to-BAM",
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stemcellcommons
parents:
diff changeset
337 "outputs": [
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stemcellcommons
parents:
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338 {
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stemcellcommons
parents:
diff changeset
339 "name": "output1",
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stemcellcommons
parents:
diff changeset
340 "type": "bam"
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diff changeset
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diff changeset
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diff changeset
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stemcellcommons
parents:
diff changeset
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stemcellcommons
parents:
diff changeset
349 "action_arguments": {},
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stemcellcommons
parents:
diff changeset
350 "action_type": "HideDatasetAction",
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stemcellcommons
parents:
diff changeset
351 "output_name": "output1"
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stemcellcommons
parents:
diff changeset
352 }
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diff changeset
353 },
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stemcellcommons
parents:
diff changeset
354 "tool_errors": null,
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stemcellcommons
parents:
diff changeset
355 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1",
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stemcellcommons
parents:
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parents:
diff changeset
357 "tool_version": "2.1",
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parents:
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358 "type": "tool",
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parents:
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stemcellcommons
parents:
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360 "workflow_outputs": []
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stemcellcommons
parents:
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parents:
diff changeset
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stemcellcommons
parents:
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363 "annotation": "",
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stemcellcommons
parents:
diff changeset
364 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1",
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stemcellcommons
parents:
diff changeset
365 "id": 7,
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stemcellcommons
parents:
diff changeset
366 "input_connections": {
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stemcellcommons
parents:
diff changeset
367 "source|input1": {
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stemcellcommons
parents:
diff changeset
368 "id": 5,
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stemcellcommons
parents:
diff changeset
369 "output_name": "output"
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stemcellcommons
parents:
diff changeset
370 }
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stemcellcommons
parents:
diff changeset
371 },
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stemcellcommons
parents:
diff changeset
372 "inputs": [],
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stemcellcommons
parents:
diff changeset
373 "label": null,
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stemcellcommons
parents:
diff changeset
374 "name": "SAM-to-BAM",
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stemcellcommons
parents:
diff changeset
375 "outputs": [
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stemcellcommons
parents:
diff changeset
376 {
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stemcellcommons
parents:
diff changeset
377 "name": "output1",
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stemcellcommons
parents:
diff changeset
378 "type": "bam"
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stemcellcommons
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diff changeset
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stemcellcommons
parents:
diff changeset
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parents:
diff changeset
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diff changeset
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diff changeset
385 "post_job_actions": {
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stemcellcommons
parents:
diff changeset
386 "HideDatasetActionoutput1": {
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stemcellcommons
parents:
diff changeset
387 "action_arguments": {},
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stemcellcommons
parents:
diff changeset
388 "action_type": "HideDatasetAction",
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stemcellcommons
parents:
diff changeset
389 "output_name": "output1"
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stemcellcommons
parents:
diff changeset
390 }
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stemcellcommons
parents:
diff changeset
391 },
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stemcellcommons
parents:
diff changeset
392 "tool_errors": null,
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stemcellcommons
parents:
diff changeset
393 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1",
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stemcellcommons
parents:
diff changeset
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stemcellcommons
parents:
diff changeset
395 "tool_version": "2.1",
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stemcellcommons
parents:
diff changeset
396 "type": "tool",
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stemcellcommons
parents:
diff changeset
397 "uuid": "1a747633-c084-433c-8ca5-1f1196e3791f",
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stemcellcommons
parents:
diff changeset
398 "workflow_outputs": []
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stemcellcommons
parents:
diff changeset
399 },
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stemcellcommons
parents:
diff changeset
400 "8": {
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stemcellcommons
parents:
diff changeset
401 "annotation": "{\"output_tabular\": {\"name\": \"MACS2_bed\", \"description\": \"\", \"type\": \"tabular\"}, \"output_plot\": {\"name\": \"MACS2_plot\", \"description\": \"\", \"type\": \"pdf\"}}",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
402 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
403 "id": 8,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
404 "input_connections": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
405 "input_control_file": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
406 "id": 7,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
407 "output_name": "output1"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
408 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
409 "input_treatment_file": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
410 "id": 6,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
411 "output_name": "output1"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
412 }
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
413 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
414 "inputs": [],
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
415 "label": null,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
416 "name": "MACS2 callpeak",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
417 "outputs": [
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
418 {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
419 "name": "output_tabular",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
420 "type": "tabular"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
421 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
422 {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
423 "name": "output_broadpeaks",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
424 "type": "bed"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
425 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
426 {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
427 "name": "output_gappedpeaks",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
428 "type": "bed"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
429 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
430 {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
431 "name": "output_narrowpeaks",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
432 "type": "bed"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
433 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
434 {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
435 "name": "output_summits",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
436 "type": "bed"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
437 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
438 {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
439 "name": "output_plot",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
440 "type": "pdf"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
441 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
442 {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
443 "name": "output_treat_pileup",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
444 "type": "bedgraph"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
445 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
446 {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
447 "name": "output_control_lambda",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
448 "type": "bedgraph"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
449 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
450 {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
451 "name": "output_extra_files",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
452 "type": "html"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
453 }
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
454 ],
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
455 "position": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
456 "left": 1750,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
457 "top": 358.5
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
458 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
459 "post_job_actions": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
460 "HideDatasetActionoutput_broadpeaks": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
461 "action_arguments": {},
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
462 "action_type": "HideDatasetAction",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
463 "output_name": "output_broadpeaks"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
464 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
465 "HideDatasetActionoutput_control_lambda": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
466 "action_arguments": {},
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
467 "action_type": "HideDatasetAction",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
468 "output_name": "output_control_lambda"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
469 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
470 "HideDatasetActionoutput_extra_files": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
471 "action_arguments": {},
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
472 "action_type": "HideDatasetAction",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
473 "output_name": "output_extra_files"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
474 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
475 "HideDatasetActionoutput_gappedpeaks": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
476 "action_arguments": {},
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
477 "action_type": "HideDatasetAction",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
478 "output_name": "output_gappedpeaks"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
479 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
480 "HideDatasetActionoutput_narrowpeaks": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
481 "action_arguments": {},
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
482 "action_type": "HideDatasetAction",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
483 "output_name": "output_narrowpeaks"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
484 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
485 "HideDatasetActionoutput_summits": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
486 "action_arguments": {},
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
487 "action_type": "HideDatasetAction",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
488 "output_name": "output_summits"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
489 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
490 "HideDatasetActionoutput_tabular": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
491 "action_arguments": {},
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
492 "action_type": "HideDatasetAction",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
493 "output_name": "output_tabular"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
494 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
495 "HideDatasetActionoutput_treat_pileup": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
496 "action_arguments": {},
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
497 "action_type": "HideDatasetAction",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
498 "output_name": "output_treat_pileup"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
499 }
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
500 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
501 "tool_errors": null,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
502 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
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\\\"\"}",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
504 "tool_version": "2.1.0.20151222.0",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
505 "type": "tool",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
506 "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
507 "workflow_outputs": [
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
508 {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
509 "label": null,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
510 "output_name": "output_plot",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
511 "uuid": "32ac3a7b-5509-45fe-a69e-abfd2b33f0be"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
512 }
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
513 ]
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
514 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
515 "9": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
516 "annotation": "",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
517 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
518 "id": 9,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
519 "input_connections": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
520 "infile_control": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
521 "id": 8,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
522 "output_name": "output_control_lambda"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
523 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
524 "infile_treatment": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
525 "id": 8,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
526 "output_name": "output_treat_pileup"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
527 }
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
528 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
529 "inputs": [],
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
530 "label": null,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
531 "name": "MACS2 bdgcmp",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
532 "outputs": [
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
533 {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
534 "name": "outfile",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
535 "type": "bedgraph"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
536 }
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
537 ],
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
538 "position": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
539 "left": 2087.5,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
540 "top": 426.5
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
541 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
542 "post_job_actions": {},
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
543 "tool_errors": null,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
544 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
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\"}",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
546 "tool_version": "2.1.0.20151222.0",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
547 "type": "tool",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
548 "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
549 "workflow_outputs": [
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
550 {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
551 "label": null,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
552 "output_name": "outfile",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
553 "uuid": "6b9699e0-5597-4810-9e3c-1f81149ea132"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
554 }
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
555 ]
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
556 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
557 "10": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
558 "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
559 "content_id": "wig_to_bigWig",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
560 "id": 10,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
561 "input_connections": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
562 "input1": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
563 "id": 9,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
564 "output_name": "outfile"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
565 }
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
566 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
567 "inputs": [],
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
568 "label": null,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
569 "name": "Wig/BedGraph-to-bigWig",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
570 "outputs": [
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
571 {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
572 "name": "out_file1",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
573 "type": "bigwig"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
574 }
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
575 ],
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
576 "position": {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
577 "left": 2292.546875,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
578 "top": 447.71875
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
579 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
580 "post_job_actions": {},
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
581 "tool_errors": null,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
582 "tool_id": "wig_to_bigWig",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
583 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
584 "tool_version": "1.1.0",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
585 "type": "tool",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
586 "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
587 "workflow_outputs": [
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
588 {
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
589 "label": null,
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
590 "output_name": "out_file1",
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
591 "uuid": "8e824df2-af08-4fa7-bba5-221044f10c1b"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
592 }
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
593 ]
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
594 }
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
595 },
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
596 "uuid": "bf6866e8-1ed1-4684-8dbd-fc8744257dcb"
358360fdeea9 Update annotation
stemcellcommons
parents:
diff changeset
597 }