0
|
1 {
|
|
2 "a_galaxy_workflow": "true",
|
|
3 "annotation": "",
|
|
4 "format-version": "0.1",
|
11
|
5 "name": "blockclust 1.1.0 complete",
|
0
|
6 "steps": {
|
|
7 "0": {
|
|
8 "annotation": "",
|
11
|
9 "content_id": null,
|
|
10 "errors": null,
|
0
|
11 "id": 0,
|
|
12 "input_connections": {},
|
11
|
13 "inputs": [],
|
|
14 "label": "blockclust_input",
|
0
|
15 "name": "Input dataset",
|
|
16 "outputs": [],
|
|
17 "position": {
|
11
|
18 "left": 200,
|
|
19 "top": 338
|
0
|
20 },
|
|
21 "tool_id": null,
|
11
|
22 "tool_state": "{}",
|
0
|
23 "tool_version": null,
|
|
24 "type": "data_input",
|
11
|
25 "uuid": "b6e23dd8-46ca-4bd6-87f3-2f6b741b459b",
|
|
26 "workflow_outputs": [
|
|
27 {
|
|
28 "label": null,
|
|
29 "output_name": "output",
|
|
30 "uuid": "d8c12432-a0db-4cba-a815-aba6a2de9626"
|
|
31 }
|
|
32 ]
|
0
|
33 },
|
|
34 "1": {
|
|
35 "annotation": "",
|
11
|
36 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2",
|
|
37 "errors": null,
|
0
|
38 "id": 1,
|
|
39 "input_connections": {
|
11
|
40 "input1": {
|
0
|
41 "id": 0,
|
|
42 "output_name": "output"
|
|
43 }
|
|
44 },
|
11
|
45 "inputs": [
|
|
46 {
|
|
47 "description": "runtime parameter for tool Samtools sort",
|
|
48 "name": "input1"
|
|
49 }
|
|
50 ],
|
|
51 "label": null,
|
|
52 "name": "Samtools sort",
|
|
53 "outputs": [
|
|
54 {
|
|
55 "name": "output1",
|
|
56 "type": "bam"
|
|
57 }
|
|
58 ],
|
|
59 "position": {
|
|
60 "left": 460,
|
|
61 "top": 338
|
|
62 },
|
|
63 "post_job_actions": {},
|
|
64 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2",
|
|
65 "tool_shed_repository": {
|
|
66 "changeset_revision": "f56bdb93ae58",
|
|
67 "name": "samtools_sort",
|
|
68 "owner": "devteam",
|
|
69 "tool_shed": "toolshed.g2.bx.psu.edu"
|
|
70 },
|
|
71 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"prim_key_cond\": \"{\\\"prim_key_select\\\": \\\"\\\", \\\"__current_case__\\\": 0}\"}",
|
|
72 "tool_version": "2.0.2",
|
|
73 "type": "tool",
|
|
74 "uuid": "327e9b59-6d4e-482e-bcdf-c7cc5d8505c9",
|
|
75 "workflow_outputs": [
|
|
76 {
|
|
77 "label": null,
|
|
78 "output_name": "output1",
|
|
79 "uuid": "22295821-a765-4e6c-804f-6c710e26923f"
|
|
80 }
|
|
81 ]
|
|
82 },
|
|
83 "2": {
|
|
84 "annotation": "",
|
|
85 "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
|
|
86 "errors": null,
|
|
87 "id": 2,
|
|
88 "input_connections": {
|
|
89 "tool_mode|reads_bam": {
|
|
90 "id": 1,
|
|
91 "output_name": "output1"
|
|
92 }
|
|
93 },
|
|
94 "inputs": [
|
|
95 {
|
|
96 "description": "runtime parameter for tool BlockClust",
|
|
97 "name": "tool_mode"
|
|
98 }
|
|
99 ],
|
|
100 "label": null,
|
0
|
101 "name": "BlockClust",
|
|
102 "outputs": [
|
|
103 {
|
|
104 "name": "tags_bed",
|
|
105 "type": "bed"
|
|
106 },
|
|
107 {
|
|
108 "name": "hclust_plot",
|
|
109 "type": "pdf"
|
|
110 },
|
|
111 {
|
|
112 "name": "clusters",
|
|
113 "type": "bed"
|
|
114 },
|
|
115 {
|
|
116 "name": "model_based_pred_bed",
|
|
117 "type": "bed"
|
|
118 },
|
|
119 {
|
|
120 "name": "nearest_neighbour_pred_bed",
|
|
121 "type": "bed"
|
|
122 },
|
|
123 {
|
|
124 "name": "sim_tab_out",
|
|
125 "type": "tabular"
|
|
126 },
|
|
127 {
|
|
128 "name": "cluster_dist",
|
|
129 "type": "pdf"
|
|
130 },
|
|
131 {
|
|
132 "name": "cluster_hclust",
|
|
133 "type": "pdf"
|
|
134 }
|
|
135 ],
|
|
136 "position": {
|
11
|
137 "left": 788,
|
|
138 "top": 338
|
0
|
139 },
|
|
140 "post_job_actions": {
|
|
141 "HideDatasetActioncluster_dist": {
|
|
142 "action_arguments": {},
|
|
143 "action_type": "HideDatasetAction",
|
|
144 "output_name": "cluster_dist"
|
|
145 },
|
|
146 "HideDatasetActioncluster_hclust": {
|
|
147 "action_arguments": {},
|
|
148 "action_type": "HideDatasetAction",
|
|
149 "output_name": "cluster_hclust"
|
|
150 },
|
|
151 "HideDatasetActionclusters": {
|
|
152 "action_arguments": {},
|
|
153 "action_type": "HideDatasetAction",
|
|
154 "output_name": "clusters"
|
|
155 },
|
|
156 "HideDatasetActionhclust_plot": {
|
|
157 "action_arguments": {},
|
|
158 "action_type": "HideDatasetAction",
|
|
159 "output_name": "hclust_plot"
|
|
160 },
|
|
161 "HideDatasetActionmodel_based_pred_bed": {
|
|
162 "action_arguments": {},
|
|
163 "action_type": "HideDatasetAction",
|
|
164 "output_name": "model_based_pred_bed"
|
|
165 },
|
|
166 "HideDatasetActionnearest_neighbour_pred_bed": {
|
|
167 "action_arguments": {},
|
|
168 "action_type": "HideDatasetAction",
|
|
169 "output_name": "nearest_neighbour_pred_bed"
|
|
170 },
|
|
171 "HideDatasetActionsim_tab_out": {
|
|
172 "action_arguments": {},
|
|
173 "action_type": "HideDatasetAction",
|
|
174 "output_name": "sim_tab_out"
|
11
|
175 }
|
|
176 },
|
|
177 "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
|
|
178 "tool_shed_repository": {
|
|
179 "changeset_revision": "aab6cf87b40a",
|
|
180 "name": "blockclust",
|
|
181 "owner": "rnateam",
|
|
182 "tool_shed": "toolshed.g2.bx.psu.edu"
|
|
183 },
|
|
184 "tool_state": "{\"tool_mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
|
|
185 "tool_version": "1.1.0",
|
|
186 "type": "tool",
|
|
187 "uuid": "fd3043d3-609e-4303-bcb5-448cb749a319",
|
|
188 "workflow_outputs": [
|
|
189 {
|
|
190 "label": "tags_bed",
|
|
191 "output_name": "tags_bed",
|
|
192 "uuid": "39f8722a-8444-42f8-8104-f81201804c9c"
|
|
193 }
|
|
194 ]
|
|
195 },
|
|
196 "3": {
|
|
197 "annotation": "",
|
|
198 "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
|
|
199 "errors": null,
|
|
200 "id": 3,
|
|
201 "input_connections": {
|
|
202 "infile": {
|
|
203 "id": 2,
|
0
|
204 "output_name": "tags_bed"
|
|
205 }
|
|
206 },
|
11
|
207 "inputs": [
|
|
208 {
|
|
209 "description": "runtime parameter for tool Sort",
|
|
210 "name": "infile"
|
0
|
211 }
|
11
|
212 ],
|
|
213 "label": null,
|
0
|
214 "name": "Sort",
|
|
215 "outputs": [
|
|
216 {
|
11
|
217 "name": "outfile",
|
0
|
218 "type": "input"
|
|
219 }
|
|
220 ],
|
|
221 "position": {
|
11
|
222 "left": 1116,
|
|
223 "top": 338
|
0
|
224 },
|
|
225 "post_job_actions": {
|
11
|
226 "HideDatasetActionoutfile": {
|
0
|
227 "action_arguments": {},
|
|
228 "action_type": "HideDatasetAction",
|
11
|
229 "output_name": "outfile"
|
0
|
230 }
|
|
231 },
|
11
|
232 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
|
|
233 "tool_shed_repository": {
|
|
234 "changeset_revision": "74a8bef53a00",
|
|
235 "name": "text_processing",
|
|
236 "owner": "bgruening",
|
|
237 "tool_shed": "toolshed.g2.bx.psu.edu"
|
|
238 },
|
|
239 "tool_state": "{\"sortkeys\": \"[{\\\"column\\\": \\\"1\\\", \\\"__index__\\\": 0, \\\"style\\\": \\\"\\\", \\\"order\\\": \\\"\\\"}, {\\\"column\\\": \\\"6\\\", \\\"__index__\\\": 1, \\\"style\\\": \\\"\\\", \\\"order\\\": \\\"\\\"}, {\\\"column\\\": \\\"2\\\", \\\"__index__\\\": 2, \\\"style\\\": \\\"n\\\", \\\"order\\\": \\\"\\\"}, {\\\"column\\\": \\\"3\\\", \\\"__index__\\\": 3, \\\"style\\\": \\\"n\\\", \\\"order\\\": \\\"\\\"}]\", \"__page__\": null, \"ignore_case\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"header\": \"\\\"0\\\"\", \"unique\": \"\\\"false\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
|
|
240 "tool_version": "1.1.1",
|
0
|
241 "type": "tool",
|
11
|
242 "uuid": "ecaa7fb8-a10a-457c-9ce0-3b7f0647d1b4",
|
|
243 "workflow_outputs": []
|
0
|
244 },
|
11
|
245 "4": {
|
0
|
246 "annotation": "",
|
11
|
247 "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2",
|
|
248 "errors": null,
|
|
249 "id": 4,
|
0
|
250 "input_connections": {
|
|
251 "input": {
|
11
|
252 "id": 3,
|
|
253 "output_name": "outfile"
|
0
|
254 }
|
|
255 },
|
11
|
256 "inputs": [
|
|
257 {
|
|
258 "description": "runtime parameter for tool blockbuster",
|
|
259 "name": "input"
|
|
260 }
|
|
261 ],
|
|
262 "label": null,
|
0
|
263 "name": "blockbuster",
|
|
264 "outputs": [
|
|
265 {
|
|
266 "name": "output",
|
11
|
267 "type": "bed"
|
0
|
268 }
|
|
269 ],
|
|
270 "position": {
|
11
|
271 "left": 1376,
|
|
272 "top": 338
|
0
|
273 },
|
|
274 "post_job_actions": {},
|
11
|
275 "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2",
|
|
276 "tool_shed_repository": {
|
|
277 "changeset_revision": "7c7ff7a3503f",
|
|
278 "name": "blockbuster",
|
|
279 "owner": "rnateam",
|
|
280 "tool_shed": "toolshed.g2.bx.psu.edu"
|
|
281 },
|
|
282 "tool_state": "{\"distance\": \"\\\"40\\\"\", \"scale\": \"\\\"0.5\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"print\": \"\\\"bbf_reads\\\"\", \"tagFilter\": \"\\\"0\\\"\", \"merge\": \"\\\"0\\\"\", \"minBlockHeight\": \"\\\"1.0\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"minClusterHeight\": \"\\\"50.0\\\"\"}",
|
|
283 "tool_version": "0.1.2",
|
0
|
284 "type": "tool",
|
11
|
285 "uuid": "8a3db40c-ae03-49ca-b47c-559ac455d712",
|
|
286 "workflow_outputs": [
|
|
287 {
|
|
288 "label": "blockbuster_out",
|
|
289 "output_name": "output",
|
|
290 "uuid": "95c21ce9-e988-44b9-978e-10a27b74d18e"
|
|
291 }
|
|
292 ]
|
0
|
293 },
|
11
|
294 "5": {
|
0
|
295 "annotation": "",
|
11
|
296 "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
|
|
297 "errors": null,
|
|
298 "id": 5,
|
0
|
299 "input_connections": {
|
|
300 "tool_mode|input_bbo": {
|
11
|
301 "id": 4,
|
0
|
302 "output_name": "output"
|
|
303 }
|
|
304 },
|
|
305 "inputs": [
|
|
306 {
|
|
307 "description": "runtime parameter for tool BlockClust",
|
|
308 "name": "tool_mode"
|
11
|
309 },
|
|
310 {
|
|
311 "description": "runtime parameter for tool BlockClust",
|
|
312 "name": "tool_mode"
|
0
|
313 }
|
|
314 ],
|
11
|
315 "label": null,
|
0
|
316 "name": "BlockClust",
|
|
317 "outputs": [
|
|
318 {
|
|
319 "name": "tags_bed",
|
|
320 "type": "bed"
|
|
321 },
|
|
322 {
|
|
323 "name": "hclust_plot",
|
|
324 "type": "pdf"
|
|
325 },
|
|
326 {
|
|
327 "name": "clusters",
|
|
328 "type": "bed"
|
|
329 },
|
|
330 {
|
|
331 "name": "model_based_pred_bed",
|
|
332 "type": "bed"
|
|
333 },
|
|
334 {
|
|
335 "name": "nearest_neighbour_pred_bed",
|
|
336 "type": "bed"
|
|
337 },
|
|
338 {
|
|
339 "name": "sim_tab_out",
|
|
340 "type": "tabular"
|
|
341 },
|
|
342 {
|
|
343 "name": "cluster_dist",
|
|
344 "type": "pdf"
|
|
345 },
|
|
346 {
|
|
347 "name": "cluster_hclust",
|
|
348 "type": "pdf"
|
|
349 }
|
|
350 ],
|
|
351 "position": {
|
11
|
352 "left": 1694,
|
|
353 "top": 338
|
0
|
354 },
|
|
355 "post_job_actions": {
|
|
356 "HideDatasetActioncluster_dist": {
|
|
357 "action_arguments": {},
|
|
358 "action_type": "HideDatasetAction",
|
|
359 "output_name": "cluster_dist"
|
|
360 },
|
|
361 "HideDatasetActioncluster_hclust": {
|
|
362 "action_arguments": {},
|
|
363 "action_type": "HideDatasetAction",
|
|
364 "output_name": "cluster_hclust"
|
|
365 },
|
|
366 "HideDatasetActionsim_tab_out": {
|
|
367 "action_arguments": {},
|
|
368 "action_type": "HideDatasetAction",
|
|
369 "output_name": "sim_tab_out"
|
|
370 },
|
|
371 "HideDatasetActiontags_bed": {
|
|
372 "action_arguments": {},
|
|
373 "action_type": "HideDatasetAction",
|
|
374 "output_name": "tags_bed"
|
|
375 }
|
|
376 },
|
11
|
377 "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
|
|
378 "tool_shed_repository": {
|
|
379 "changeset_revision": "aab6cf87b40a",
|
|
380 "name": "blockclust",
|
|
381 "owner": "rnateam",
|
|
382 "tool_shed": "toolshed.g2.bx.psu.edu"
|
|
383 },
|
|
384 "tool_state": "{\"tool_mode\": \"{\\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"input_bbo\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"pred\\\": {\\\"pred_mode\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"enable_pred\\\": \\\"yes\\\"}, \\\"nochr\\\": \\\"false\\\", \\\"__current_case__\\\": 1, \\\"operation\\\": \\\"analysis\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
|
|
385 "tool_version": "1.1.0",
|
0
|
386 "type": "tool",
|
11
|
387 "uuid": "e41a16eb-4edd-4f9e-b615-44d0c2988b63",
|
|
388 "workflow_outputs": [
|
|
389 {
|
|
390 "label": "clusters_bed",
|
|
391 "output_name": "clusters",
|
|
392 "uuid": "287b4bae-55a1-4f38-b1c3-62ae60b4d950"
|
|
393 },
|
|
394 {
|
|
395 "label": "nn_based_pred_bed",
|
|
396 "output_name": "nearest_neighbour_pred_bed",
|
|
397 "uuid": "b9761d55-2b95-4ee6-82e3-d6b3dab75b13"
|
|
398 },
|
|
399 {
|
|
400 "label": null,
|
|
401 "output_name": "hclust_plot",
|
|
402 "uuid": "01744525-c294-4534-814d-547e87f7cc49"
|
|
403 },
|
|
404 {
|
|
405 "label": "model_based_pred_bed",
|
|
406 "output_name": "model_based_pred_bed",
|
|
407 "uuid": "d5172432-a088-489e-828c-7e6346339441"
|
|
408 }
|
|
409 ]
|
0
|
410 },
|
11
|
411 "6": {
|
0
|
412 "annotation": "",
|
11
|
413 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3",
|
|
414 "errors": null,
|
|
415 "id": 6,
|
0
|
416 "input_connections": {
|
|
417 "input": {
|
11
|
418 "id": 5,
|
0
|
419 "output_name": "clusters"
|
|
420 }
|
|
421 },
|
11
|
422 "inputs": [
|
|
423 {
|
|
424 "description": "runtime parameter for tool Extract Genomic DNA",
|
|
425 "name": "interpret_features"
|
|
426 },
|
|
427 {
|
|
428 "description": "runtime parameter for tool Extract Genomic DNA",
|
|
429 "name": "input"
|
|
430 },
|
|
431 {
|
|
432 "description": "runtime parameter for tool Extract Genomic DNA",
|
|
433 "name": "reference_genome_cond"
|
|
434 }
|
|
435 ],
|
|
436 "label": null,
|
0
|
437 "name": "Extract Genomic DNA",
|
|
438 "outputs": [
|
|
439 {
|
11
|
440 "name": "output",
|
0
|
441 "type": "input"
|
|
442 }
|
|
443 ],
|
|
444 "position": {
|
11
|
445 "left": 2022,
|
|
446 "top": 338
|
0
|
447 },
|
|
448 "post_job_actions": {
|
11
|
449 "HideDatasetActionoutput": {
|
0
|
450 "action_arguments": {},
|
|
451 "action_type": "HideDatasetAction",
|
11
|
452 "output_name": "output"
|
0
|
453 }
|
|
454 },
|
11
|
455 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3",
|
|
456 "tool_shed_repository": {
|
|
457 "changeset_revision": "e400dcbc60d0",
|
|
458 "name": "extract_genomic_dna",
|
|
459 "owner": "iuc",
|
|
460 "tool_shed": "toolshed.g2.bx.psu.edu"
|
|
461 },
|
|
462 "tool_state": "{\"__page__\": null, \"output_format_cond\": \"{\\\"fasta_header_type_cond\\\": {\\\"fasta_header_type\\\": \\\"char_delimited\\\", \\\"fasta_header_delimiter\\\": \\\"underscore\\\", \\\"__current_case__\\\": 1}, \\\"output_format\\\": \\\"fasta\\\", \\\"__current_case__\\\": 0}\", \"interpret_features\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"reference_genome_cond\": \"{\\\"reference_genome\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_genome_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
|
|
463 "tool_version": "3.0.3",
|
0
|
464 "type": "tool",
|
11
|
465 "uuid": "fb82ac27-7e3e-4640-b743-4b96c962a53a",
|
|
466 "workflow_outputs": []
|
0
|
467 },
|
11
|
468 "7": {
|
0
|
469 "annotation": "",
|
11
|
470 "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0",
|
|
471 "errors": null,
|
|
472 "id": 7,
|
0
|
473 "input_connections": {
|
|
474 "seqdb": {
|
11
|
475 "id": 6,
|
|
476 "output_name": "output"
|
0
|
477 }
|
|
478 },
|
11
|
479 "inputs": [
|
|
480 {
|
|
481 "description": "runtime parameter for tool cmsearch",
|
|
482 "name": "seqdb"
|
|
483 }
|
|
484 ],
|
|
485 "label": null,
|
|
486 "name": "cmsearch",
|
0
|
487 "outputs": [
|
|
488 {
|
|
489 "name": "outfile",
|
|
490 "type": "tabular"
|
|
491 },
|
|
492 {
|
|
493 "name": "multiple_alignment_output",
|
|
494 "type": "tabular"
|
|
495 }
|
|
496 ],
|
|
497 "position": {
|
11
|
498 "left": 2311,
|
|
499 "top": 340
|
0
|
500 },
|
|
501 "post_job_actions": {
|
|
502 "HideDatasetActionmultiple_alignment_output": {
|
|
503 "action_arguments": {},
|
|
504 "action_type": "HideDatasetAction",
|
|
505 "output_name": "multiple_alignment_output"
|
|
506 },
|
|
507 "HideDatasetActionoutfile": {
|
|
508 "action_arguments": {},
|
|
509 "action_type": "HideDatasetAction",
|
|
510 "output_name": "outfile"
|
|
511 }
|
|
512 },
|
11
|
513 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0",
|
|
514 "tool_shed_repository": {
|
|
515 "changeset_revision": "477d829d3250",
|
|
516 "name": "infernal",
|
|
517 "owner": "bgruening",
|
|
518 "tool_shed": "toolshed.g2.bx.psu.edu"
|
|
519 },
|
|
520 "tool_state": "{\"A\": \"\\\"false\\\"\", \"verbose\": \"\\\"false\\\"\", \"notrunc\": \"\\\"false\\\"\", \"smxsize\": \"\\\"128.0\\\"\", \"cm_opts\": \"{\\\"database\\\": \\\"rfam_11_0\\\", \\\"__current_case__\\\": 0, \\\"cm_opts_selector\\\": \\\"db\\\"}\", \"__page__\": null, \"bottomonly\": \"\\\"false\\\"\", \"seqdb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"inclusion_thresholds_opts\": \"{\\\"__current_case__\\\": 0, \\\"inclusion_thresholds_selector\\\": \\\"\\\"}\", \"__rerun_remap_job_id__\": null, \"mxsize\": \"\\\"128.0\\\"\", \"anytrunc\": \"\\\"false\\\"\", \"acyk\": \"\\\"false\\\"\", \"acceleration_huristics\": \"{\\\"__current_case__\\\": 3, \\\"acceleration_huristics_selector\\\": \\\"--default\\\"}\", \"reporting_thresholds_opts\": \"{\\\"reporting_thresholds_selector\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"cyk\": \"\\\"false\\\"\", \"Z\": \"\\\"\\\"\", \"model_thresholds\": \"{\\\"cut_ga\\\": \\\"false\\\", \\\"cut_nc\\\": \\\"false\\\", \\\"cut_tc\\\": \\\"false\\\"}\", \"g\": \"\\\"false\\\"\", \"nonull3\": \"\\\"false\\\"\", \"toponly\": \"\\\"false\\\"\", \"noali\": \"\\\"false\\\"\"}",
|
|
521 "tool_version": "1.1.2.0",
|
0
|
522 "type": "tool",
|
11
|
523 "uuid": "842f09a0-b91c-4a9b-a3a5-019f0fda1aba",
|
|
524 "workflow_outputs": []
|
0
|
525 },
|
11
|
526 "8": {
|
0
|
527 "annotation": "",
|
11
|
528 "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
|
|
529 "errors": null,
|
|
530 "id": 8,
|
0
|
531 "input_connections": {
|
|
532 "tool_mode|clusters_bed": {
|
11
|
533 "id": 5,
|
0
|
534 "output_name": "clusters"
|
|
535 },
|
|
536 "tool_mode|cmsearch_out": {
|
11
|
537 "id": 7,
|
0
|
538 "output_name": "outfile"
|
|
539 },
|
|
540 "tool_mode|sim_tab_in": {
|
11
|
541 "id": 5,
|
0
|
542 "output_name": "sim_tab_out"
|
|
543 }
|
|
544 },
|
11
|
545 "inputs": [
|
|
546 {
|
|
547 "description": "runtime parameter for tool BlockClust",
|
|
548 "name": "tool_mode"
|
|
549 },
|
|
550 {
|
|
551 "description": "runtime parameter for tool BlockClust",
|
|
552 "name": "tool_mode"
|
|
553 },
|
|
554 {
|
|
555 "description": "runtime parameter for tool BlockClust",
|
|
556 "name": "tool_mode"
|
|
557 }
|
|
558 ],
|
|
559 "label": null,
|
0
|
560 "name": "BlockClust",
|
|
561 "outputs": [
|
|
562 {
|
|
563 "name": "tags_bed",
|
|
564 "type": "bed"
|
|
565 },
|
|
566 {
|
|
567 "name": "hclust_plot",
|
|
568 "type": "pdf"
|
|
569 },
|
|
570 {
|
|
571 "name": "clusters",
|
|
572 "type": "bed"
|
|
573 },
|
|
574 {
|
|
575 "name": "model_based_pred_bed",
|
|
576 "type": "bed"
|
|
577 },
|
|
578 {
|
|
579 "name": "nearest_neighbour_pred_bed",
|
|
580 "type": "bed"
|
|
581 },
|
|
582 {
|
|
583 "name": "sim_tab_out",
|
|
584 "type": "tabular"
|
|
585 },
|
|
586 {
|
|
587 "name": "cluster_dist",
|
|
588 "type": "pdf"
|
|
589 },
|
|
590 {
|
|
591 "name": "cluster_hclust",
|
|
592 "type": "pdf"
|
|
593 }
|
|
594 ],
|
|
595 "position": {
|
11
|
596 "left": 2639,
|
|
597 "top": 338
|
0
|
598 },
|
|
599 "post_job_actions": {
|
|
600 "HideDatasetActionclusters": {
|
|
601 "action_arguments": {},
|
|
602 "action_type": "HideDatasetAction",
|
|
603 "output_name": "clusters"
|
|
604 },
|
|
605 "HideDatasetActionhclust_plot": {
|
|
606 "action_arguments": {},
|
|
607 "action_type": "HideDatasetAction",
|
|
608 "output_name": "hclust_plot"
|
|
609 },
|
|
610 "HideDatasetActionmodel_based_pred_bed": {
|
|
611 "action_arguments": {},
|
|
612 "action_type": "HideDatasetAction",
|
|
613 "output_name": "model_based_pred_bed"
|
|
614 },
|
|
615 "HideDatasetActionnearest_neighbour_pred_bed": {
|
|
616 "action_arguments": {},
|
|
617 "action_type": "HideDatasetAction",
|
|
618 "output_name": "nearest_neighbour_pred_bed"
|
|
619 },
|
|
620 "HideDatasetActionsim_tab_out": {
|
|
621 "action_arguments": {},
|
|
622 "action_type": "HideDatasetAction",
|
|
623 "output_name": "sim_tab_out"
|
|
624 },
|
|
625 "HideDatasetActiontags_bed": {
|
|
626 "action_arguments": {},
|
|
627 "action_type": "HideDatasetAction",
|
|
628 "output_name": "tags_bed"
|
|
629 }
|
|
630 },
|
11
|
631 "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
|
|
632 "tool_shed_repository": {
|
|
633 "changeset_revision": "aab6cf87b40a",
|
|
634 "name": "blockclust",
|
|
635 "owner": "rnateam",
|
|
636 "tool_shed": "toolshed.g2.bx.psu.edu"
|
|
637 },
|
|
638 "tool_state": "{\"tool_mode\": \"{\\\"cmsearch_out\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"operation\\\": \\\"post\\\", \\\"clusters_bed\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 2, \\\"sim_tab_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
|
|
639 "tool_version": "1.1.0",
|
0
|
640 "type": "tool",
|
11
|
641 "uuid": "dfdaf591-1d6f-45f0-bf05-4fac5680155e",
|
|
642 "workflow_outputs": [
|
|
643 {
|
|
644 "label": null,
|
|
645 "output_name": "cluster_hclust",
|
|
646 "uuid": "75860090-3020-4281-9887-b73389b9c207"
|
|
647 },
|
|
648 {
|
|
649 "label": null,
|
|
650 "output_name": "cluster_dist",
|
|
651 "uuid": "c749ddcc-628b-4e46-a61d-dfbe00901964"
|
|
652 }
|
|
653 ]
|
0
|
654 }
|
11
|
655 },
|
|
656 "tags": [],
|
|
657 "uuid": "a60be50d-44e1-4fb5-90a0-3b849ceaf3e3"
|
0
|
658 } |