comparison MACS2_SPP_ChIP-Seq.ga @ 0:8d4be9af8a51 draft default tip

Uploaded
author stemcellcommons
date Tue, 28 Jan 2014 11:30:42 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:8d4be9af8a51
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": "MACS2+SPP ChIP-Seq = groomer + bowtie + filter + cut + igvtools",
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": 299.75,
21 "top": 300.140625
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": 299.75,
44 "top": 491.140625
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": 500.4375,
72 "top": 299.328125
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": 499.5,
101 "top": 490
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": 799.75,
146 "top": 299.140625
147 },
148 "post_job_actions": {},
149 "tool_errors": null,
150 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.2",
151 "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"dm3\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sUnmappedFile\\\": \\\"False\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSeed\\\": \\\"-1\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sMaqSoapAlign\\\": \\\"-1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sTryHard\\\": \\\"noTryHard\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sdStrata\\\": \\\"noStrata\\\", \\\"sdMaxBacktracks\\\": \\\"800\\\", \\\"sBest\\\": \\\"doBest\\\", \\\"__current_case__\\\": 1}, \\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeedLen\\\": \\\"28\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"sMaxFile\\\": \\\"False\\\"}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}",
152 "tool_version": "1.1.2",
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": 800.75,
191 "top": 493.140625
192 },
193 "post_job_actions": {},
194 "tool_errors": null,
195 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.2",
196 "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"dm3\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sUnmappedFile\\\": \\\"False\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSeed\\\": \\\"-1\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sMaqSoapAlign\\\": \\\"-1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sTryHard\\\": \\\"noTryHard\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sdStrata\\\": \\\"noStrata\\\", \\\"sdMaxBacktracks\\\": \\\"800\\\", \\\"sBest\\\": \\\"doBest\\\", \\\"__current_case__\\\": 1}, \\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeedLen\\\": \\\"28\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"sMaxFile\\\": \\\"False\\\"}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}",
197 "tool_version": "1.1.2",
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": 1142.25,
220 "top": 326.640625
221 },
222 "post_job_actions": {},
223 "tool_errors": null,
224 "tool_id": "sam_to_bam",
225 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
226 "tool_version": "1.1.2",
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": 1135.25,
249 "top": 520.125
250 },
251 "post_job_actions": {},
252 "tool_errors": null,
253 "tool_id": "sam_to_bam",
254 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
255 "tool_version": "1.1.2",
256 "type": "tool",
257 "user_outputs": []
258 },
259 "8": {
260 "annotation": "{\"output_tdf\": {\"name\": \"igv_count_1\", \"description\": \"\", \"type\": \"tdf\"}}",
261 "id": 8,
262 "input_connections": {
263 "input": {
264 "id": 6,
265 "output_name": "output1"
266 }
267 },
268 "inputs": [],
269 "name": "IGVtools count",
270 "outputs": [
271 {
272 "name": "output_tdf",
273 "type": "igv.tdf"
274 },
275 {
276 "name": "output_wig",
277 "type": "wig"
278 }
279 ],
280 "position": {
281 "left": 1575.75,
282 "top": 220.140625
283 },
284 "post_job_actions": {},
285 "tool_errors": null,
286 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_count/1.0",
287 "tool_state": "{\"__page__\": 0, \"extend\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"zoom\": \"\\\"7\\\"\", \"window\": \"\\\"25\\\"\", \"output_fmt\": \"\\\"output.tdf\\\"\", \"input\": \"null\", \"refGenomeSource\": \"{\\\"refGenomeSource_type\\\": \\\"built-in\\\", \\\"ref\\\": \\\"/n/hsphS10/hsphfs1/chb/biodata/genomes/igv/dm3.genome\\\", \\\"__current_case__\\\": 0}\", \"window_functions\": \"\\\"mean\\\"\"}",
288 "tool_version": "1.0",
289 "type": "tool",
290 "user_outputs": []
291 },
292 "9": {
293 "annotation": "",
294 "id": 9,
295 "input_connections": {
296 "major_command|input_chipseq_file1": {
297 "id": 6,
298 "output_name": "output1"
299 },
300 "major_command|input_control_file1": {
301 "id": 7,
302 "output_name": "output1"
303 }
304 },
305 "inputs": [],
306 "name": "SPP",
307 "outputs": [
308 {
309 "name": "output_default_file",
310 "type": "txt"
311 },
312 {
313 "name": "output_narrow_peak",
314 "type": "txt"
315 },
316 {
317 "name": "output_plot_file",
318 "type": "pdf"
319 },
320 {
321 "name": "output_region_peak",
322 "type": "txt"
323 },
324 {
325 "name": "output_peakshift_file",
326 "type": "txt"
327 },
328 {
329 "name": "output_rdata_file",
330 "type": "txt"
331 }
332 ],
333 "position": {
334 "left": 1573,
335 "top": 365
336 },
337 "post_job_actions": {},
338 "tool_errors": null,
339 "tool_id": "toolshed.g2.bx.psu.edu/repos/stemcellcommons/spp_tool/spp_peak_calling/1.11.0",
340 "tool_state": "{\"major_command\": \"{\\\"save_plot_file\\\": \\\"True\\\", \\\"input_chipseq_file1\\\": null, \\\"replace\\\": \\\"True\\\", \\\"num_peaks\\\": \\\"0\\\", \\\"major_command_selector\\\": \\\"peak_calling\\\", \\\"save_rdata_file\\\": \\\"False\\\", \\\"input_control_file1\\\": null, \\\"__current_case__\\\": 1, \\\"save_regionpeak_file\\\": \\\"True\\\", \\\"save_narrowpeak_file\\\": \\\"True\\\", \\\"fdr\\\": \\\"0.1\\\"}\", \"__page__\": 0, \"experiment_name\": \"\\\"SPP in Galaxy\\\"\", \"__rerun_remap_job_id__\": null}",
341 "tool_version": "1.11.0",
342 "type": "tool",
343 "user_outputs": []
344 },
345 "10": {
346 "annotation": "{\"output_tdf\": {\"name\": \"igv_count_2\", \"description\": \"\", \"type\": \"tdf\"}}",
347 "id": 10,
348 "input_connections": {
349 "input": {
350 "id": 7,
351 "output_name": "output1"
352 }
353 },
354 "inputs": [],
355 "name": "IGVtools count",
356 "outputs": [
357 {
358 "name": "output_tdf",
359 "type": "igv.tdf"
360 },
361 {
362 "name": "output_wig",
363 "type": "wig"
364 }
365 ],
366 "position": {
367 "left": 1575.75,
368 "top": 642.140625
369 },
370 "post_job_actions": {},
371 "tool_errors": null,
372 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_count/1.0",
373 "tool_state": "{\"__page__\": 0, \"extend\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"zoom\": \"\\\"7\\\"\", \"window\": \"\\\"25\\\"\", \"output_fmt\": \"\\\"output.tdf\\\"\", \"input\": \"null\", \"refGenomeSource\": \"{\\\"refGenomeSource_type\\\": \\\"built-in\\\", \\\"ref\\\": \\\"/n/hsphS10/hsphfs1/chb/biodata/genomes/igv/danRer7.genome\\\", \\\"__current_case__\\\": 0}\", \"window_functions\": \"\\\"mean\\\"\"}",
374 "tool_version": "1.0",
375 "type": "tool",
376 "user_outputs": []
377 },
378 "11": {
379 "annotation": "",
380 "id": 11,
381 "input_connections": {
382 "major_command|input_chipseq_file1": {
383 "id": 6,
384 "output_name": "output1"
385 },
386 "major_command|input_control_file1": {
387 "id": 7,
388 "output_name": "output1"
389 }
390 },
391 "inputs": [],
392 "name": "MACS2",
393 "outputs": [
394 {
395 "name": "output_bed_file",
396 "type": "bed"
397 },
398 {
399 "name": "output_extra_files",
400 "type": "html"
401 },
402 {
403 "name": "output_peaks_file",
404 "type": "xls"
405 },
406 {
407 "name": "output_narrowpeaks_file",
408 "type": "txt"
409 },
410 {
411 "name": "output_xls_to_interval_peaks_file",
412 "type": "interval"
413 },
414 {
415 "name": "output_xls_to_interval_negative_peaks_file",
416 "type": "interval"
417 },
418 {
419 "name": "output_bdgcmp_file",
420 "type": "bdg"
421 }
422 ],
423 "position": {
424 "left": 1574,
425 "top": 786
426 },
427 "post_job_actions": {},
428 "tool_errors": null,
429 "tool_id": "toolshed.g2.bx.psu.edu/repos/stemcellcommons/macs2/macs2_peakcalling/2.0.10",
430 "tool_state": "{\"major_command\": \"{\\\"gsize\\\": \\\"1400000000.0\\\", \\\"bdg\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"advanced_options\\\": {\\\"mfoldlo\\\": \\\"10\\\", \\\"nolambda\\\": \\\"False\\\", \\\"advanced_options_selector\\\": \\\"on\\\", \\\"mfoldhi\\\": \\\"30\\\", \\\"__current_case__\\\": 0}, \\\"input_chipseq_file1\\\": null, \\\"xls_to_interval\\\": \\\"False\\\", \\\"major_command_selector\\\": \\\"callpeak\\\", \\\"input_control_file1\\\": null, \\\"pq_options\\\": {\\\"pq_options_selector\\\": \\\"qvalue\\\", \\\"qvalue\\\": \\\"0.05\\\", \\\"__current_case__\\\": 1}, \\\"bw\\\": \\\"200\\\", \\\"nomodel_type\\\": {\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 1}}\", \"__page__\": 0, \"experiment_name\": \"\\\"MACS2 in Galaxy\\\"\", \"__rerun_remap_job_id__\": null}",
431 "tool_version": "2.0.10",
432 "type": "tool",
433 "user_outputs": []
434 },
435 "12": {
436 "annotation": "",
437 "id": 12,
438 "input_connections": {
439 "input": {
440 "id": 9,
441 "output_name": "output_narrow_peak"
442 }
443 },
444 "inputs": [],
445 "name": "Cut",
446 "outputs": [
447 {
448 "name": "out_file1",
449 "type": "tabular"
450 }
451 ],
452 "position": {
453 "left": 1818.75,
454 "top": 321.140625
455 },
456 "post_job_actions": {
457 "ChangeDatatypeActionout_file1": {
458 "action_arguments": {
459 "newtype": "bed"
460 },
461 "action_type": "ChangeDatatypeAction",
462 "output_name": "out_file1"
463 }
464 },
465 "tool_errors": null,
466 "tool_id": "Cut1",
467 "tool_state": "{\"columnList\": \"\\\"c1,c2,c3,c4,c7\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
468 "tool_version": "1.0.2",
469 "type": "tool",
470 "user_outputs": []
471 },
472 "13": {
473 "annotation": "",
474 "id": 13,
475 "input_connections": {
476 "input": {
477 "id": 9,
478 "output_name": "output_region_peak"
479 }
480 },
481 "inputs": [],
482 "name": "Cut",
483 "outputs": [
484 {
485 "name": "out_file1",
486 "type": "tabular"
487 }
488 ],
489 "position": {
490 "left": 1810.734375,
491 "top": 554.125
492 },
493 "post_job_actions": {
494 "ChangeDatatypeActionout_file1": {
495 "action_arguments": {
496 "newtype": "bed"
497 },
498 "action_type": "ChangeDatatypeAction",
499 "output_name": "out_file1"
500 }
501 },
502 "tool_errors": null,
503 "tool_id": "Cut1",
504 "tool_state": "{\"columnList\": \"\\\"c1,c2,c3,c4,c7\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
505 "tool_version": "1.0.2",
506 "type": "tool",
507 "user_outputs": []
508 },
509 "14": {
510 "annotation": "",
511 "id": 14,
512 "input_connections": {
513 "input": {
514 "id": 11,
515 "output_name": "output_bed_file"
516 }
517 },
518 "inputs": [],
519 "name": "IGVtools sort",
520 "outputs": [
521 {
522 "name": "output_sam",
523 "type": "sam"
524 },
525 {
526 "name": "output_bed",
527 "type": "sam"
528 },
529 {
530 "name": "output_vcf",
531 "type": "sam"
532 },
533 {
534 "name": "output_psl",
535 "type": "sam"
536 },
537 {
538 "name": "output_igv",
539 "type": "sam"
540 },
541 {
542 "name": "output_cn",
543 "type": "sam"
544 }
545 ],
546 "position": {
547 "left": 2023.9375,
548 "top": 880.9375
549 },
550 "post_job_actions": {},
551 "tool_errors": null,
552 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_sort/1.0",
553 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
554 "tool_version": "1.0",
555 "type": "tool",
556 "user_outputs": []
557 },
558 "15": {
559 "annotation": "{\"out_file1\": {\"name\": \"spp_filtered_narrowpeak\", \"description\": \"\", \"type\": \"txt\"}}",
560 "id": 15,
561 "input_connections": {
562 "input": {
563 "id": 12,
564 "output_name": "out_file1"
565 }
566 },
567 "inputs": [],
568 "name": "Filter",
569 "outputs": [
570 {
571 "name": "out_file1",
572 "type": "input"
573 }
574 ],
575 "position": {
576 "left": 1838.1875,
577 "top": 440.8125
578 },
579 "post_job_actions": {},
580 "tool_errors": null,
581 "tool_id": "Filter1",
582 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c5>15\\\"\", \"__page__\": 0}",
583 "tool_version": "1.1.0",
584 "type": "tool",
585 "user_outputs": []
586 },
587 "16": {
588 "annotation": "{\"out_file1\": {\"name\": \"spp_filtered_regionpeak\", \"description\": \"\", \"type\": \"txt\"}}",
589 "id": 16,
590 "input_connections": {
591 "input": {
592 "id": 13,
593 "output_name": "out_file1"
594 }
595 },
596 "inputs": [],
597 "name": "Filter",
598 "outputs": [
599 {
600 "name": "out_file1",
601 "type": "input"
602 }
603 ],
604 "position": {
605 "left": 1818.25,
606 "top": 663.859375
607 },
608 "post_job_actions": {},
609 "tool_errors": null,
610 "tool_id": "Filter1",
611 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c5>15\\\"\", \"__page__\": 0}",
612 "tool_version": "1.1.0",
613 "type": "tool",
614 "user_outputs": []
615 },
616 "17": {
617 "annotation": "{\"output_tdf\": {\"name\": \"igv_count_5\", \"description\": \"\", \"type\": \"tdf\"}}",
618 "id": 17,
619 "input_connections": {
620 "input": {
621 "id": 14,
622 "output_name": "output_bed"
623 }
624 },
625 "inputs": [],
626 "name": "IGVtools count",
627 "outputs": [
628 {
629 "name": "output_tdf",
630 "type": "igv.tdf"
631 },
632 {
633 "name": "output_wig",
634 "type": "wig"
635 }
636 ],
637 "position": {
638 "left": 2358.265625,
639 "top": 882.09375
640 },
641 "post_job_actions": {},
642 "tool_errors": null,
643 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_count/1.0",
644 "tool_state": "{\"__page__\": 0, \"extend\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"zoom\": \"\\\"7\\\"\", \"window\": \"\\\"25\\\"\", \"output_fmt\": \"\\\"output.tdf\\\"\", \"input\": \"null\", \"refGenomeSource\": \"{\\\"refGenomeSource_type\\\": \\\"built-in\\\", \\\"ref\\\": \\\"/n/hsphS10/hsphfs1/chb/biodata/genomes/igv/dm3.genome\\\", \\\"__current_case__\\\": 0}\", \"window_functions\": \"\\\"mean\\\"\"}",
645 "tool_version": "1.0",
646 "type": "tool",
647 "user_outputs": []
648 },
649 "18": {
650 "annotation": "",
651 "id": 18,
652 "input_connections": {
653 "input": {
654 "id": 15,
655 "output_name": "out_file1"
656 }
657 },
658 "inputs": [],
659 "name": "IGVtools sort",
660 "outputs": [
661 {
662 "name": "output_sam",
663 "type": "sam"
664 },
665 {
666 "name": "output_bed",
667 "type": "sam"
668 },
669 {
670 "name": "output_vcf",
671 "type": "sam"
672 },
673 {
674 "name": "output_psl",
675 "type": "sam"
676 },
677 {
678 "name": "output_igv",
679 "type": "sam"
680 },
681 {
682 "name": "output_cn",
683 "type": "sam"
684 }
685 ],
686 "position": {
687 "left": 2026.75,
688 "top": 231.140625
689 },
690 "post_job_actions": {},
691 "tool_errors": null,
692 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_sort/1.0",
693 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
694 "tool_version": "1.0",
695 "type": "tool",
696 "user_outputs": []
697 },
698 "19": {
699 "annotation": "",
700 "id": 19,
701 "input_connections": {
702 "input": {
703 "id": 16,
704 "output_name": "out_file1"
705 }
706 },
707 "inputs": [],
708 "name": "IGVtools sort",
709 "outputs": [
710 {
711 "name": "output_sam",
712 "type": "sam"
713 },
714 {
715 "name": "output_bed",
716 "type": "sam"
717 },
718 {
719 "name": "output_vcf",
720 "type": "sam"
721 },
722 {
723 "name": "output_psl",
724 "type": "sam"
725 },
726 {
727 "name": "output_igv",
728 "type": "sam"
729 },
730 {
731 "name": "output_cn",
732 "type": "sam"
733 }
734 ],
735 "position": {
736 "left": 2021.75,
737 "top": 554.140625
738 },
739 "post_job_actions": {},
740 "tool_errors": null,
741 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_sort/1.0",
742 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
743 "tool_version": "1.0",
744 "type": "tool",
745 "user_outputs": []
746 },
747 "20": {
748 "annotation": "{\"output_tdf\": {\"name\": \"igv_count_3\", \"description\": \"\", \"type\": \"tdf\"}}",
749 "id": 20,
750 "input_connections": {
751 "input": {
752 "id": 18,
753 "output_name": "output_bed"
754 }
755 },
756 "inputs": [],
757 "name": "IGVtools count",
758 "outputs": [
759 {
760 "name": "output_tdf",
761 "type": "igv.tdf"
762 },
763 {
764 "name": "output_wig",
765 "type": "wig"
766 }
767 ],
768 "position": {
769 "left": 2338.75,
770 "top": 337.140625
771 },
772 "post_job_actions": {},
773 "tool_errors": null,
774 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_count/1.0",
775 "tool_state": "{\"__page__\": 0, \"extend\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"zoom\": \"\\\"7\\\"\", \"window\": \"\\\"25\\\"\", \"output_fmt\": \"\\\"output.tdf\\\"\", \"input\": \"null\", \"refGenomeSource\": \"{\\\"refGenomeSource_type\\\": \\\"built-in\\\", \\\"ref\\\": \\\"/n/hsphS10/hsphfs1/chb/biodata/genomes/igv/dm3.genome\\\", \\\"__current_case__\\\": 0}\", \"window_functions\": \"\\\"mean\\\"\"}",
776 "tool_version": "1.0",
777 "type": "tool",
778 "user_outputs": []
779 },
780 "21": {
781 "annotation": "{\"output_tdf\": {\"name\": \"igv_count_4\", \"description\": \"\", \"type\": \"tdf\"}}",
782 "id": 21,
783 "input_connections": {
784 "input": {
785 "id": 19,
786 "output_name": "output_bed"
787 }
788 },
789 "inputs": [],
790 "name": "IGVtools count",
791 "outputs": [
792 {
793 "name": "output_tdf",
794 "type": "igv.tdf"
795 },
796 {
797 "name": "output_wig",
798 "type": "wig"
799 }
800 ],
801 "position": {
802 "left": 2345.75,
803 "top": 567.140625
804 },
805 "post_job_actions": {},
806 "tool_errors": null,
807 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_count/1.0",
808 "tool_state": "{\"__page__\": 0, \"extend\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"zoom\": \"\\\"7\\\"\", \"window\": \"\\\"25\\\"\", \"output_fmt\": \"\\\"output.tdf\\\"\", \"input\": \"null\", \"refGenomeSource\": \"{\\\"refGenomeSource_type\\\": \\\"built-in\\\", \\\"ref\\\": \\\"/n/hsphS10/hsphfs1/chb/biodata/genomes/igv/dm3.genome\\\", \\\"__current_case__\\\": 0}\", \"window_functions\": \"\\\"mean\\\"\"}",
809 "tool_version": "1.0",
810 "type": "tool",
811 "user_outputs": []
812 }
813 }
814 }