comparison spp_(modencode)-fastq-bowtie-igvtools_mm9-chr19.ga @ 0:ca5d1fdea504 draft default tip

Uploaded
author hackdna
date Wed, 01 May 2013 18:12:47 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:ca5d1fdea504
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "{\"refinery_type\": \"analysis\", \"refinery_relationships\": [{\"category\":\"1-1\", \"set1\":\"tag file\", \"set2\":\"control file\"}]}",
4 "format-version": "0.1",
5 "name": "spp (modencode) + fastq + cut + igvtools: mm9-chr19",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "",
14 "name": "tag file"
15 }
16 ],
17 "name": "Input dataset",
18 "outputs": [],
19 "position": {
20 "left": 200,
21 "top": 363
22 },
23 "tool_errors": null,
24 "tool_id": null,
25 "tool_state": "{\"name\": \"tag 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": "control file"
38 }
39 ],
40 "name": "Input dataset",
41 "outputs": [],
42 "position": {
43 "left": 200,
44 "top": 554
45 },
46 "tool_errors": null,
47 "tool_id": null,
48 "tool_state": "{\"name\": \"control 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 Groomer",
64 "outputs": [
65 {
66 "name": "output_file",
67 "type": "fastqsanger"
68 }
69 ],
70 "position": {
71 "left": 400,
72 "top": 366
73 },
74 "post_job_actions": {
75 "HideDatasetActionoutput_file": {
76 "action_arguments": {},
77 "action_type": "HideDatasetAction",
78 "output_name": "output_file"
79 }
80 },
81 "tool_errors": null,
82 "tool_id": "fastq_groomer",
83 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"options_type_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1, \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"null\"}",
84 "tool_version": "1.0.4",
85 "type": "tool",
86 "user_outputs": []
87 },
88 "3": {
89 "annotation": "",
90 "id": 3,
91 "input_connections": {
92 "input_file": {
93 "id": 1,
94 "output_name": "output"
95 }
96 },
97 "inputs": [],
98 "name": "FASTQ Groomer",
99 "outputs": [
100 {
101 "name": "output_file",
102 "type": "fastqsanger"
103 }
104 ],
105 "position": {
106 "left": 401,
107 "top": 559
108 },
109 "post_job_actions": {
110 "HideDatasetActionoutput_file": {
111 "action_arguments": {},
112 "action_type": "HideDatasetAction",
113 "output_name": "output_file"
114 }
115 },
116 "tool_errors": null,
117 "tool_id": "fastq_groomer",
118 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"options_type_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1, \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"null\"}",
119 "tool_version": "1.0.4",
120 "type": "tool",
121 "user_outputs": []
122 },
123 "4": {
124 "annotation": "",
125 "id": 4,
126 "input_connections": {
127 "singlePaired|sInput1": {
128 "id": 2,
129 "output_name": "output_file"
130 }
131 },
132 "inputs": [],
133 "name": "Map with Bowtie for Illumina",
134 "outputs": [
135 {
136 "name": "output",
137 "type": "sam"
138 },
139 {
140 "name": "output_suppressed_reads_l",
141 "type": "fastq"
142 },
143 {
144 "name": "output_suppressed_reads_r",
145 "type": "fastq"
146 },
147 {
148 "name": "output_unmapped_reads_l",
149 "type": "fastq"
150 },
151 {
152 "name": "output_unmapped_reads_r",
153 "type": "fastq"
154 }
155 ],
156 "position": {
157 "left": 708,
158 "top": 369
159 },
160 "post_job_actions": {
161 "HideDatasetActionoutput": {
162 "action_arguments": {},
163 "action_type": "HideDatasetAction",
164 "output_name": "output"
165 },
166 "HideDatasetActionoutput_suppressed_reads_l": {
167 "action_arguments": {},
168 "action_type": "HideDatasetAction",
169 "output_name": "output_suppressed_reads_l"
170 },
171 "HideDatasetActionoutput_suppressed_reads_r": {
172 "action_arguments": {},
173 "action_type": "HideDatasetAction",
174 "output_name": "output_suppressed_reads_r"
175 },
176 "HideDatasetActionoutput_unmapped_reads_l": {
177 "action_arguments": {},
178 "action_type": "HideDatasetAction",
179 "output_name": "output_unmapped_reads_l"
180 },
181 "HideDatasetActionoutput_unmapped_reads_r": {
182 "action_arguments": {},
183 "action_type": "HideDatasetAction",
184 "output_name": "output_unmapped_reads_r"
185 }
186 },
187 "tool_errors": null,
188 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.2",
189 "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm9-chr19\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sSettingsType\\\": \\\"preSet\\\", \\\"__current_case__\\\": 0}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}",
190 "tool_version": "1.1.2",
191 "type": "tool",
192 "user_outputs": []
193 },
194 "5": {
195 "annotation": "",
196 "id": 5,
197 "input_connections": {
198 "singlePaired|sInput1": {
199 "id": 3,
200 "output_name": "output_file"
201 }
202 },
203 "inputs": [],
204 "name": "Map with Bowtie for Illumina",
205 "outputs": [
206 {
207 "name": "output",
208 "type": "sam"
209 },
210 {
211 "name": "output_suppressed_reads_l",
212 "type": "fastq"
213 },
214 {
215 "name": "output_suppressed_reads_r",
216 "type": "fastq"
217 },
218 {
219 "name": "output_unmapped_reads_l",
220 "type": "fastq"
221 },
222 {
223 "name": "output_unmapped_reads_r",
224 "type": "fastq"
225 }
226 ],
227 "position": {
228 "left": 707,
229 "top": 559
230 },
231 "post_job_actions": {
232 "HideDatasetActionoutput": {
233 "action_arguments": {},
234 "action_type": "HideDatasetAction",
235 "output_name": "output"
236 },
237 "HideDatasetActionoutput_suppressed_reads_l": {
238 "action_arguments": {},
239 "action_type": "HideDatasetAction",
240 "output_name": "output_suppressed_reads_l"
241 },
242 "HideDatasetActionoutput_suppressed_reads_r": {
243 "action_arguments": {},
244 "action_type": "HideDatasetAction",
245 "output_name": "output_suppressed_reads_r"
246 },
247 "HideDatasetActionoutput_unmapped_reads_l": {
248 "action_arguments": {},
249 "action_type": "HideDatasetAction",
250 "output_name": "output_unmapped_reads_l"
251 },
252 "HideDatasetActionoutput_unmapped_reads_r": {
253 "action_arguments": {},
254 "action_type": "HideDatasetAction",
255 "output_name": "output_unmapped_reads_r"
256 }
257 },
258 "tool_errors": null,
259 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.2",
260 "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm9-chr19\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sSettingsType\\\": \\\"preSet\\\", \\\"__current_case__\\\": 0}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}",
261 "tool_version": "1.1.2",
262 "type": "tool",
263 "user_outputs": []
264 },
265 "6": {
266 "annotation": "",
267 "id": 6,
268 "input_connections": {
269 "source|input1": {
270 "id": 4,
271 "output_name": "output"
272 }
273 },
274 "inputs": [],
275 "name": "SAM-to-BAM",
276 "outputs": [
277 {
278 "name": "output1",
279 "type": "bam"
280 }
281 ],
282 "position": {
283 "left": 992,
284 "top": 371
285 },
286 "post_job_actions": {
287 "HideDatasetActionoutput1": {
288 "action_arguments": {},
289 "action_type": "HideDatasetAction",
290 "output_name": "output1"
291 }
292 },
293 "tool_errors": null,
294 "tool_id": "sam_to_bam",
295 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__page__\": 0}",
296 "tool_version": "1.1.2",
297 "type": "tool",
298 "user_outputs": []
299 },
300 "7": {
301 "annotation": "",
302 "id": 7,
303 "input_connections": {
304 "source|input1": {
305 "id": 5,
306 "output_name": "output"
307 }
308 },
309 "inputs": [],
310 "name": "SAM-to-BAM",
311 "outputs": [
312 {
313 "name": "output1",
314 "type": "bam"
315 }
316 ],
317 "position": {
318 "left": 993,
319 "top": 561
320 },
321 "post_job_actions": {
322 "HideDatasetActionoutput1": {
323 "action_arguments": {},
324 "action_type": "HideDatasetAction",
325 "output_name": "output1"
326 }
327 },
328 "tool_errors": null,
329 "tool_id": "sam_to_bam",
330 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__page__\": 0}",
331 "tool_version": "1.1.2",
332 "type": "tool",
333 "user_outputs": []
334 },
335 "8": {
336 "annotation": "{\"output_tdf\": {\"name\":\"igvtools_count_01\", \"description\":\"\", \"type\":\"tdf\"}}",
337 "id": 8,
338 "input_connections": {
339 "input": {
340 "id": 6,
341 "output_name": "output1"
342 }
343 },
344 "inputs": [],
345 "name": "IGVtools count",
346 "outputs": [
347 {
348 "name": "output_tdf",
349 "type": "igv.tdf"
350 },
351 {
352 "name": "output_wig",
353 "type": "wig"
354 }
355 ],
356 "position": {
357 "left": 1214,
358 "top": 306
359 },
360 "post_job_actions": {
361 "HideDatasetActionoutput_tdf": {
362 "action_arguments": {},
363 "action_type": "HideDatasetAction",
364 "output_name": "output_tdf"
365 },
366 "HideDatasetActionoutput_wig": {
367 "action_arguments": {},
368 "action_type": "HideDatasetAction",
369 "output_name": "output_wig"
370 }
371 },
372 "tool_errors": null,
373 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_count/1.0",
374 "tool_state": "{\"__page__\": 0, \"extend\": \"\\\"\\\"\", \"zoom\": \"\\\"7\\\"\", \"window\": \"\\\"25\\\"\", \"output_fmt\": \"\\\"output.tdf\\\"\", \"input\": \"null\", \"refGenomeSource\": \"{\\\"refGenomeSource_type\\\": \\\"built-in\\\", \\\"ref\\\": \\\"/n/hsphS10/hsphfs1/chb/biodata/genomes/igv/mm9.genome\\\", \\\"__current_case__\\\": 0}\", \"window_functions\": \"\\\"mean\\\"\"}",
375 "tool_version": "1.0",
376 "type": "tool",
377 "user_outputs": []
378 },
379 "9": {
380 "annotation": "{\"output_default_file\": {\"name\":\"spp_default_file\", \"description\":\"\", \"type\":\"txt\"}, \"output_narrow_peak\": {\"name\":\"spp_narrow_peak\", \"description\":\"\", \"type\":\"txt\"}, \"output_plot_file\": {\"name\":\"spp_plot_file\", \"description\":\"\", \"type\":\"pdf\"}, \"output_region_peak\": {\"name\":\"spp_region_peak\", \"description\":\"\", \"type\":\"txt\"}}",
381 "id": 9,
382 "input_connections": {
383 "major_command|input_chipseq_file1": {
384 "id": 6,
385 "output_name": "output1"
386 },
387 "major_command|input_control_file1": {
388 "id": 7,
389 "output_name": "output1"
390 }
391 },
392 "inputs": [],
393 "name": "SPP",
394 "outputs": [
395 {
396 "name": "output_default_file",
397 "type": "txt"
398 },
399 {
400 "name": "output_narrow_peak",
401 "type": "txt"
402 },
403 {
404 "name": "output_plot_file",
405 "type": "pdf"
406 },
407 {
408 "name": "output_region_peak",
409 "type": "txt"
410 },
411 {
412 "name": "output_peakshift_file",
413 "type": "txt"
414 },
415 {
416 "name": "output_rdata_file",
417 "type": "txt"
418 }
419 ],
420 "position": {
421 "left": 1202,
422 "top": 470
423 },
424 "post_job_actions": {
425 "HideDatasetActionoutput_default_file": {
426 "action_arguments": {},
427 "action_type": "HideDatasetAction",
428 "output_name": "output_default_file"
429 },
430 "HideDatasetActionoutput_narrow_peak": {
431 "action_arguments": {},
432 "action_type": "HideDatasetAction",
433 "output_name": "output_narrow_peak"
434 },
435 "HideDatasetActionoutput_peakshift_file": {
436 "action_arguments": {},
437 "action_type": "HideDatasetAction",
438 "output_name": "output_peakshift_file"
439 },
440 "HideDatasetActionoutput_plot_file": {
441 "action_arguments": {},
442 "action_type": "HideDatasetAction",
443 "output_name": "output_plot_file"
444 },
445 "HideDatasetActionoutput_rdata_file": {
446 "action_arguments": {},
447 "action_type": "HideDatasetAction",
448 "output_name": "output_rdata_file"
449 },
450 "HideDatasetActionoutput_region_peak": {
451 "action_arguments": {},
452 "action_type": "HideDatasetAction",
453 "output_name": "output_region_peak"
454 }
455 },
456 "tool_errors": null,
457 "tool_id": "toolshed.g2.bx.psu.edu/repos/modencode-dcc/spp_package/modencode_peakcalling_spp/1.10.1",
458 "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\\\": \\\"True\\\", \\\"input_control_file1\\\": null, \\\"__current_case__\\\": 1, \\\"save_regionpeak_file\\\": \\\"True\\\", \\\"save_narrowpeak_file\\\": \\\"True\\\", \\\"fdr\\\": \\\"0\\\"}\", \"__page__\": 0, \"experiment_name\": \"\\\"SPP in Galaxy\\\"\"}",
459 "tool_version": "1.10.1",
460 "type": "tool",
461 "user_outputs": []
462 },
463 "10": {
464 "annotation": "{\"output_tdf\": {\"name\":\"igvtools_count_02\", \"description\":\"\", \"type\":\"tdf\"}}",
465 "id": 10,
466 "input_connections": {
467 "input": {
468 "id": 7,
469 "output_name": "output1"
470 }
471 },
472 "inputs": [],
473 "name": "IGVtools count",
474 "outputs": [
475 {
476 "name": "output_tdf",
477 "type": "igv.tdf"
478 },
479 {
480 "name": "output_wig",
481 "type": "wig"
482 }
483 ],
484 "position": {
485 "left": 1223,
486 "top": 750
487 },
488 "post_job_actions": {
489 "HideDatasetActionoutput_tdf": {
490 "action_arguments": {},
491 "action_type": "HideDatasetAction",
492 "output_name": "output_tdf"
493 },
494 "HideDatasetActionoutput_wig": {
495 "action_arguments": {},
496 "action_type": "HideDatasetAction",
497 "output_name": "output_wig"
498 }
499 },
500 "tool_errors": null,
501 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_count/1.0",
502 "tool_state": "{\"__page__\": 0, \"extend\": \"\\\"\\\"\", \"zoom\": \"\\\"7\\\"\", \"window\": \"\\\"25\\\"\", \"output_fmt\": \"\\\"output.tdf\\\"\", \"input\": \"null\", \"refGenomeSource\": \"{\\\"refGenomeSource_type\\\": \\\"built-in\\\", \\\"ref\\\": \\\"/n/hsphS10/hsphfs1/chb/biodata/genomes/igv/mm9.genome\\\", \\\"__current_case__\\\": 0}\", \"window_functions\": \"\\\"mean\\\"\"}",
503 "tool_version": "1.0",
504 "type": "tool",
505 "user_outputs": []
506 },
507 "11": {
508 "annotation": "",
509 "id": 11,
510 "input_connections": {
511 "input": {
512 "id": 9,
513 "output_name": "output_narrow_peak"
514 }
515 },
516 "inputs": [],
517 "name": "Cut",
518 "outputs": [
519 {
520 "name": "out_file1",
521 "type": "tabular"
522 }
523 ],
524 "position": {
525 "left": 1469,
526 "top": 394
527 },
528 "post_job_actions": {
529 "ChangeDatatypeActionout_file1": {
530 "action_arguments": {
531 "newtype": "bed"
532 },
533 "action_type": "ChangeDatatypeAction",
534 "output_name": "out_file1"
535 },
536 "HideDatasetActionout_file1": {
537 "action_arguments": {},
538 "action_type": "HideDatasetAction",
539 "output_name": "out_file1"
540 }
541 },
542 "tool_errors": null,
543 "tool_id": "Cut1",
544 "tool_state": "{\"columnList\": \"\\\"c1,c2,c3\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__page__\": 0}",
545 "tool_version": "1.0.1",
546 "type": "tool",
547 "user_outputs": []
548 },
549 "12": {
550 "annotation": "",
551 "id": 12,
552 "input_connections": {
553 "input": {
554 "id": 9,
555 "output_name": "output_region_peak"
556 }
557 },
558 "inputs": [],
559 "name": "Cut",
560 "outputs": [
561 {
562 "name": "out_file1",
563 "type": "tabular"
564 }
565 ],
566 "position": {
567 "left": 1474,
568 "top": 631
569 },
570 "post_job_actions": {
571 "ChangeDatatypeActionout_file1": {
572 "action_arguments": {
573 "newtype": "bed"
574 },
575 "action_type": "ChangeDatatypeAction",
576 "output_name": "out_file1"
577 },
578 "HideDatasetActionout_file1": {
579 "action_arguments": {},
580 "action_type": "HideDatasetAction",
581 "output_name": "out_file1"
582 }
583 },
584 "tool_errors": null,
585 "tool_id": "Cut1",
586 "tool_state": "{\"columnList\": \"\\\"c1,c2,c3\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__page__\": 0}",
587 "tool_version": "1.0.1",
588 "type": "tool",
589 "user_outputs": []
590 },
591 "13": {
592 "annotation": "",
593 "id": 13,
594 "input_connections": {
595 "input": {
596 "id": 11,
597 "output_name": "out_file1"
598 }
599 },
600 "inputs": [],
601 "name": "IGVtools sort",
602 "outputs": [
603 {
604 "name": "output_sam",
605 "type": "sam"
606 },
607 {
608 "name": "output_bed",
609 "type": "sam"
610 },
611 {
612 "name": "output_vcf",
613 "type": "sam"
614 },
615 {
616 "name": "output_psl",
617 "type": "sam"
618 },
619 {
620 "name": "output_igv",
621 "type": "sam"
622 },
623 {
624 "name": "output_cn",
625 "type": "sam"
626 }
627 ],
628 "position": {
629 "left": 1682,
630 "top": 282
631 },
632 "post_job_actions": {
633 "HideDatasetActionoutput_bed": {
634 "action_arguments": {},
635 "action_type": "HideDatasetAction",
636 "output_name": "output_bed"
637 },
638 "HideDatasetActionoutput_cn": {
639 "action_arguments": {},
640 "action_type": "HideDatasetAction",
641 "output_name": "output_cn"
642 },
643 "HideDatasetActionoutput_igv": {
644 "action_arguments": {},
645 "action_type": "HideDatasetAction",
646 "output_name": "output_igv"
647 },
648 "HideDatasetActionoutput_psl": {
649 "action_arguments": {},
650 "action_type": "HideDatasetAction",
651 "output_name": "output_psl"
652 },
653 "HideDatasetActionoutput_sam": {
654 "action_arguments": {},
655 "action_type": "HideDatasetAction",
656 "output_name": "output_sam"
657 },
658 "HideDatasetActionoutput_vcf": {
659 "action_arguments": {},
660 "action_type": "HideDatasetAction",
661 "output_name": "output_vcf"
662 }
663 },
664 "tool_errors": null,
665 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_sort/1.0",
666 "tool_state": "{\"input\": \"null\", \"__page__\": 0}",
667 "tool_version": "1.0",
668 "type": "tool",
669 "user_outputs": []
670 },
671 "14": {
672 "annotation": "",
673 "id": 14,
674 "input_connections": {
675 "input": {
676 "id": 12,
677 "output_name": "out_file1"
678 }
679 },
680 "inputs": [],
681 "name": "IGVtools sort",
682 "outputs": [
683 {
684 "name": "output_sam",
685 "type": "sam"
686 },
687 {
688 "name": "output_bed",
689 "type": "sam"
690 },
691 {
692 "name": "output_vcf",
693 "type": "sam"
694 },
695 {
696 "name": "output_psl",
697 "type": "sam"
698 },
699 {
700 "name": "output_igv",
701 "type": "sam"
702 },
703 {
704 "name": "output_cn",
705 "type": "sam"
706 }
707 ],
708 "position": {
709 "left": 1685,
710 "top": 617
711 },
712 "post_job_actions": {
713 "HideDatasetActionoutput_bed": {
714 "action_arguments": {},
715 "action_type": "HideDatasetAction",
716 "output_name": "output_bed"
717 },
718 "HideDatasetActionoutput_cn": {
719 "action_arguments": {},
720 "action_type": "HideDatasetAction",
721 "output_name": "output_cn"
722 },
723 "HideDatasetActionoutput_igv": {
724 "action_arguments": {},
725 "action_type": "HideDatasetAction",
726 "output_name": "output_igv"
727 },
728 "HideDatasetActionoutput_psl": {
729 "action_arguments": {},
730 "action_type": "HideDatasetAction",
731 "output_name": "output_psl"
732 },
733 "HideDatasetActionoutput_sam": {
734 "action_arguments": {},
735 "action_type": "HideDatasetAction",
736 "output_name": "output_sam"
737 },
738 "HideDatasetActionoutput_vcf": {
739 "action_arguments": {},
740 "action_type": "HideDatasetAction",
741 "output_name": "output_vcf"
742 }
743 },
744 "tool_errors": null,
745 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_sort/1.0",
746 "tool_state": "{\"input\": \"null\", \"__page__\": 0}",
747 "tool_version": "1.0",
748 "type": "tool",
749 "user_outputs": []
750 },
751 "15": {
752 "annotation": "{\"output_tdf\": {\"name\":\"igvtools_count_03\", \"description\":\"\", \"type\":\"tdf\"}}",
753 "id": 15,
754 "input_connections": {
755 "input": {
756 "id": 13,
757 "output_name": "output_bed"
758 }
759 },
760 "inputs": [],
761 "name": "IGVtools count",
762 "outputs": [
763 {
764 "name": "output_tdf",
765 "type": "igv.tdf"
766 },
767 {
768 "name": "output_wig",
769 "type": "wig"
770 }
771 ],
772 "position": {
773 "left": 2000,
774 "top": 403
775 },
776 "post_job_actions": {
777 "HideDatasetActionoutput_tdf": {
778 "action_arguments": {},
779 "action_type": "HideDatasetAction",
780 "output_name": "output_tdf"
781 },
782 "HideDatasetActionoutput_wig": {
783 "action_arguments": {},
784 "action_type": "HideDatasetAction",
785 "output_name": "output_wig"
786 }
787 },
788 "tool_errors": null,
789 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_count/1.0",
790 "tool_state": "{\"__page__\": 0, \"extend\": \"\\\"\\\"\", \"zoom\": \"\\\"7\\\"\", \"window\": \"\\\"25\\\"\", \"output_fmt\": \"\\\"output.tdf\\\"\", \"input\": \"null\", \"refGenomeSource\": \"{\\\"refGenomeSource_type\\\": \\\"built-in\\\", \\\"ref\\\": \\\"/n/hsphS10/hsphfs1/chb/biodata/genomes/igv/mm9.genome\\\", \\\"__current_case__\\\": 0}\", \"window_functions\": \"\\\"mean\\\"\"}",
791 "tool_version": "1.0",
792 "type": "tool",
793 "user_outputs": []
794 },
795 "16": {
796 "annotation": "{\"output_tdf\": {\"name\":\"igvtools_count_04\", \"description\":\"\", \"type\":\"tdf\"}}",
797 "id": 16,
798 "input_connections": {
799 "input": {
800 "id": 14,
801 "output_name": "output_bed"
802 }
803 },
804 "inputs": [],
805 "name": "IGVtools count",
806 "outputs": [
807 {
808 "name": "output_tdf",
809 "type": "igv.tdf"
810 },
811 {
812 "name": "output_wig",
813 "type": "wig"
814 }
815 ],
816 "position": {
817 "left": 1997,
818 "top": 620
819 },
820 "post_job_actions": {},
821 "tool_errors": null,
822 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools/igvtools_count/1.0",
823 "tool_state": "{\"__page__\": 0, \"extend\": \"\\\"\\\"\", \"zoom\": \"\\\"7\\\"\", \"window\": \"\\\"25\\\"\", \"output_fmt\": \"\\\"output.tdf\\\"\", \"input\": \"null\", \"refGenomeSource\": \"{\\\"refGenomeSource_type\\\": \\\"built-in\\\", \\\"ref\\\": \\\"/n/hsphS10/hsphfs1/chb/biodata/genomes/igv/mm9.genome\\\", \\\"__current_case__\\\": 0}\", \"window_functions\": \"\\\"mean\\\"\"}",
824 "tool_version": "1.0",
825 "type": "tool",
826 "user_outputs": []
827 }
828 }
829 }