comparison blockclust_workflow.ga @ 11:1e6d0af8c450 draft

blockclust workflows 1.1.0
author rnateam
date Mon, 10 Dec 2018 10:46:24 -0500
parents b2040467dad2
children
comparison
equal deleted inserted replaced
10:69fd3011b1a9 11:1e6d0af8c450
1 { 1 {
2 "a_galaxy_workflow": "true", 2 "a_galaxy_workflow": "true",
3 "annotation": "", 3 "annotation": "",
4 "format-version": "0.1", 4 "format-version": "0.1",
5 "name": "BlockClustWorkflow", 5 "name": "blockclust 1.1.0 complete",
6 "steps": { 6 "steps": {
7 "0": { 7 "0": {
8 "annotation": "", 8 "annotation": "",
9 "content_id": null,
10 "errors": null,
9 "id": 0, 11 "id": 0,
10 "input_connections": {}, 12 "input_connections": {},
11 "inputs": [ 13 "inputs": [],
12 { 14 "label": "blockclust_input",
13 "description": "",
14 "name": "Input BAM file"
15 }
16 ],
17 "name": "Input dataset", 15 "name": "Input dataset",
18 "outputs": [], 16 "outputs": [],
19 "position": { 17 "position": {
20 "left": 267, 18 "left": 200,
21 "top": 257.5 19 "top": 338
22 }, 20 },
23 "tool_errors": null,
24 "tool_id": null, 21 "tool_id": null,
25 "tool_state": "{\"name\": \"Input BAM file\"}", 22 "tool_state": "{}",
26 "tool_version": null, 23 "tool_version": null,
27 "type": "data_input", 24 "type": "data_input",
28 "user_outputs": [] 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 ]
29 }, 33 },
30 "1": { 34 "1": {
31 "annotation": "", 35 "annotation": "",
36 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2",
37 "errors": null,
32 "id": 1, 38 "id": 1,
33 "input_connections": { 39 "input_connections": {
34 "tool_mode|reads_bam": { 40 "input1": {
35 "id": 0, 41 "id": 0,
36 "output_name": "output" 42 "output_name": "output"
37 } 43 }
38 }, 44 },
39 "inputs": [], 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,
40 "name": "BlockClust", 101 "name": "BlockClust",
41 "outputs": [ 102 "outputs": [
42 { 103 {
43 "name": "tags_bed", 104 "name": "tags_bed",
44 "type": "bed" 105 "type": "bed"
71 "name": "cluster_hclust", 132 "name": "cluster_hclust",
72 "type": "pdf" 133 "type": "pdf"
73 } 134 }
74 ], 135 ],
75 "position": { 136 "position": {
76 "left": 524, 137 "left": 788,
77 "top": 323 138 "top": 338
78 }, 139 },
79 "post_job_actions": { 140 "post_job_actions": {
80 "HideDatasetActioncluster_dist": { 141 "HideDatasetActioncluster_dist": {
81 "action_arguments": {}, 142 "action_arguments": {},
82 "action_type": "HideDatasetAction", 143 "action_type": "HideDatasetAction",
109 }, 170 },
110 "HideDatasetActionsim_tab_out": { 171 "HideDatasetActionsim_tab_out": {
111 "action_arguments": {}, 172 "action_arguments": {},
112 "action_type": "HideDatasetAction", 173 "action_type": "HideDatasetAction",
113 "output_name": "sim_tab_out" 174 "output_name": "sim_tab_out"
114 }, 175 }
115 "HideDatasetActiontags_bed": { 176 },
116 "action_arguments": {}, 177 "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
117 "action_type": "HideDatasetAction", 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,
118 "output_name": "tags_bed" 204 "output_name": "tags_bed"
119 } 205 }
120 }, 206 },
121 "tool_errors": null, 207 "inputs": [
122 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", 208 {
123 "tool_state": "{\"tool_mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\", \"__page__\": 0}", 209 "description": "runtime parameter for tool Sort",
124 "tool_version": "1.0.0", 210 "name": "infile"
125 "type": "tool", 211 }
126 "user_outputs": [] 212 ],
127 }, 213 "label": null,
128 "2": { 214 "name": "Sort",
129 "annotation": "", 215 "outputs": [
130 "id": 2, 216 {
217 "name": "outfile",
218 "type": "input"
219 }
220 ],
221 "position": {
222 "left": 1116,
223 "top": 338
224 },
225 "post_job_actions": {
226 "HideDatasetActionoutfile": {
227 "action_arguments": {},
228 "action_type": "HideDatasetAction",
229 "output_name": "outfile"
230 }
231 },
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",
241 "type": "tool",
242 "uuid": "ecaa7fb8-a10a-457c-9ce0-3b7f0647d1b4",
243 "workflow_outputs": []
244 },
245 "4": {
246 "annotation": "",
247 "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2",
248 "errors": null,
249 "id": 4,
131 "input_connections": { 250 "input_connections": {
132 "input": { 251 "input": {
133 "id": 1, 252 "id": 3,
134 "output_name": "tags_bed" 253 "output_name": "outfile"
135 } 254 }
136 }, 255 },
137 "inputs": [], 256 "inputs": [
138 "name": "Sort", 257 {
139 "outputs": [ 258 "description": "runtime parameter for tool blockbuster",
140 { 259 "name": "input"
141 "name": "out_file1", 260 }
142 "type": "input" 261 ],
143 } 262 "label": null,
144 ],
145 "position": {
146 "left": 797,
147 "top": 355
148 },
149 "post_job_actions": {
150 "HideDatasetActionout_file1": {
151 "action_arguments": {},
152 "action_type": "HideDatasetAction",
153 "output_name": "out_file1"
154 }
155 },
156 "tool_errors": null,
157 "tool_id": "sort1",
158 "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[{\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 0, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}, \\\"other_style\\\": \\\"alpha\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 1, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"other_style\\\": \\\"num\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 2, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}, \\\"other_style\\\": \\\"num\\\"}]\"}",
159 "tool_version": "1.0.3",
160 "type": "tool",
161 "user_outputs": []
162 },
163 "3": {
164 "annotation": "",
165 "id": 3,
166 "input_connections": {
167 "input": {
168 "id": 2,
169 "output_name": "out_file1"
170 }
171 },
172 "inputs": [],
173 "name": "blockbuster", 263 "name": "blockbuster",
174 "outputs": [ 264 "outputs": [
175 { 265 {
176 "name": "output", 266 "name": "output",
177 "type": "tabular" 267 "type": "bed"
178 } 268 }
179 ], 269 ],
180 "position": { 270 "position": {
181 "left": 970, 271 "left": 1376,
182 "top": 225 272 "top": 338
183 }, 273 },
184 "post_job_actions": {}, 274 "post_job_actions": {},
185 "tool_errors": null, 275 "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2",
186 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1", 276 "tool_shed_repository": {
187 "tool_state": "{\"distance\": \"\\\"40\\\"\", \"scale\": \"\\\"0.5\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"print\": \"\\\"2\\\"\", \"tagFilter\": \"\\\"0\\\"\", \"merge\": \"\\\"0\\\"\", \"minBlockHeight\": \"\\\"1.0\\\"\", \"input\": \"null\", \"minClusterHeight\": \"\\\"50.0\\\"\"}", 277 "changeset_revision": "7c7ff7a3503f",
188 "tool_version": "0.1", 278 "name": "blockbuster",
189 "type": "tool", 279 "owner": "rnateam",
190 "user_outputs": [] 280 "tool_shed": "toolshed.g2.bx.psu.edu"
191 }, 281 },
192 "4": { 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\\\"\"}",
193 "annotation": "", 283 "tool_version": "0.1.2",
194 "id": 4, 284 "type": "tool",
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 ]
293 },
294 "5": {
295 "annotation": "",
296 "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
297 "errors": null,
298 "id": 5,
195 "input_connections": { 299 "input_connections": {
196 "tool_mode|input_bbo": { 300 "tool_mode|input_bbo": {
197 "id": 3, 301 "id": 4,
198 "output_name": "output" 302 "output_name": "output"
199 } 303 }
200 }, 304 },
201 "inputs": [ 305 "inputs": [
202 { 306 {
203 "description": "runtime parameter for tool BlockClust", 307 "description": "runtime parameter for tool BlockClust",
204 "name": "tool_mode" 308 "name": "tool_mode"
205 } 309 },
206 ], 310 {
311 "description": "runtime parameter for tool BlockClust",
312 "name": "tool_mode"
313 }
314 ],
315 "label": null,
207 "name": "BlockClust", 316 "name": "BlockClust",
208 "outputs": [ 317 "outputs": [
209 { 318 {
210 "name": "tags_bed", 319 "name": "tags_bed",
211 "type": "bed" 320 "type": "bed"
238 "name": "cluster_hclust", 347 "name": "cluster_hclust",
239 "type": "pdf" 348 "type": "pdf"
240 } 349 }
241 ], 350 ],
242 "position": { 351 "position": {
243 "left": 1232, 352 "left": 1694,
244 "top": 321 353 "top": 338
245 }, 354 },
246 "post_job_actions": { 355 "post_job_actions": {
247 "HideDatasetActioncluster_dist": { 356 "HideDatasetActioncluster_dist": {
248 "action_arguments": {}, 357 "action_arguments": {},
249 "action_type": "HideDatasetAction", 358 "action_type": "HideDatasetAction",
252 "HideDatasetActioncluster_hclust": { 361 "HideDatasetActioncluster_hclust": {
253 "action_arguments": {}, 362 "action_arguments": {},
254 "action_type": "HideDatasetAction", 363 "action_type": "HideDatasetAction",
255 "output_name": "cluster_hclust" 364 "output_name": "cluster_hclust"
256 }, 365 },
257 "HideDatasetActionclusters": { 366 "HideDatasetActionsim_tab_out": {
258 "action_arguments": {}, 367 "action_arguments": {},
259 "action_type": "HideDatasetAction", 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 },
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",
386 "type": "tool",
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 ]
410 },
411 "6": {
412 "annotation": "",
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,
416 "input_connections": {
417 "input": {
418 "id": 5,
260 "output_name": "clusters" 419 "output_name": "clusters"
261 }, 420 }
262 "HideDatasetActionnearest_neighbour_pred_bed": { 421 },
263 "action_arguments": {}, 422 "inputs": [
264 "action_type": "HideDatasetAction", 423 {
265 "output_name": "nearest_neighbour_pred_bed" 424 "description": "runtime parameter for tool Extract Genomic DNA",
266 }, 425 "name": "interpret_features"
267 "HideDatasetActionsim_tab_out": { 426 },
268 "action_arguments": {}, 427 {
269 "action_type": "HideDatasetAction", 428 "description": "runtime parameter for tool Extract Genomic DNA",
270 "output_name": "sim_tab_out" 429 "name": "input"
271 }, 430 },
272 "HideDatasetActiontags_bed": { 431 {
273 "action_arguments": {}, 432 "description": "runtime parameter for tool Extract Genomic DNA",
274 "action_type": "HideDatasetAction", 433 "name": "reference_genome_cond"
275 "output_name": "tags_bed" 434 }
276 } 435 ],
277 }, 436 "label": null,
278 "tool_errors": null,
279 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0",
280 "tool_state": "{\"tool_mode\": \"{\\\"pred\\\": {\\\"pred_mode\\\": \\\"model_based\\\", \\\"enable_pred\\\": \\\"yes\\\", \\\"__current_case__\\\": 0}, \\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\", \"__page__\": 0}",
281 "tool_version": "1.0.0",
282 "type": "tool",
283 "user_outputs": []
284 },
285 "5": {
286 "annotation": "",
287 "id": 5,
288 "input_connections": {
289 "input": {
290 "id": 4,
291 "output_name": "clusters"
292 }
293 },
294 "inputs": [],
295 "name": "Extract Genomic DNA", 437 "name": "Extract Genomic DNA",
296 "outputs": [ 438 "outputs": [
297 { 439 {
298 "name": "out_file1", 440 "name": "output",
299 "type": "input" 441 "type": "input"
300 } 442 }
301 ], 443 ],
302 "position": { 444 "position": {
303 "left": 1495, 445 "left": 2022,
304 "top": 248 446 "top": 338
305 }, 447 },
306 "post_job_actions": { 448 "post_job_actions": {
307 "HideDatasetActionout_file1": { 449 "HideDatasetActionoutput": {
308 "action_arguments": {}, 450 "action_arguments": {},
309 "action_type": "HideDatasetAction", 451 "action_type": "HideDatasetAction",
310 "output_name": "out_file1" 452 "output_name": "output"
311 } 453 }
312 }, 454 },
313 "tool_errors": null, 455 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3",
314 "tool_id": "Extract genomic DNA 1", 456 "tool_shed_repository": {
315 "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"yes\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\"}", 457 "changeset_revision": "e400dcbc60d0",
316 "tool_version": "2.2.3", 458 "name": "extract_genomic_dna",
317 "type": "tool", 459 "owner": "iuc",
318 "user_outputs": [] 460 "tool_shed": "toolshed.g2.bx.psu.edu"
319 }, 461 },
320 "6": { 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\\\"}\"}",
321 "annotation": "", 463 "tool_version": "3.0.3",
322 "id": 6, 464 "type": "tool",
465 "uuid": "fb82ac27-7e3e-4640-b743-4b96c962a53a",
466 "workflow_outputs": []
467 },
468 "7": {
469 "annotation": "",
470 "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0",
471 "errors": null,
472 "id": 7,
323 "input_connections": { 473 "input_connections": {
324 "seqdb": { 474 "seqdb": {
325 "id": 5, 475 "id": 6,
326 "output_name": "out_file1" 476 "output_name": "output"
327 } 477 }
328 }, 478 },
329 "inputs": [], 479 "inputs": [
330 "name": "Search covariance model(s)", 480 {
481 "description": "runtime parameter for tool cmsearch",
482 "name": "seqdb"
483 }
484 ],
485 "label": null,
486 "name": "cmsearch",
331 "outputs": [ 487 "outputs": [
332 { 488 {
333 "name": "outfile", 489 "name": "outfile",
334 "type": "tabular" 490 "type": "tabular"
335 }, 491 },
337 "name": "multiple_alignment_output", 493 "name": "multiple_alignment_output",
338 "type": "tabular" 494 "type": "tabular"
339 } 495 }
340 ], 496 ],
341 "position": { 497 "position": {
342 "left": 1753, 498 "left": 2311,
343 "top": 247 499 "top": 340
344 }, 500 },
345 "post_job_actions": { 501 "post_job_actions": {
346 "HideDatasetActionmultiple_alignment_output": { 502 "HideDatasetActionmultiple_alignment_output": {
347 "action_arguments": {}, 503 "action_arguments": {},
348 "action_type": "HideDatasetAction", 504 "action_type": "HideDatasetAction",
352 "action_arguments": {}, 508 "action_arguments": {},
353 "action_type": "HideDatasetAction", 509 "action_type": "HideDatasetAction",
354 "output_name": "outfile" 510 "output_name": "outfile"
355 } 511 }
356 }, 512 },
357 "tool_errors": null, 513 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0",
358 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.0.2", 514 "tool_shed_repository": {
359 "tool_state": "{\"A\": \"\\\"False\\\"\", \"nohmm\": \"\\\"False\\\"\", \"--acyk\": \"\\\"False\\\"\", \"bottomonly\": \"\\\"False\\\"\", \"g\": \"\\\"False\\\"\", \"inclusion_thresholds_opts\": \"{\\\"inclusion_thresholds_selector\\\": \\\"\\\", \\\"__current_case__\\\": 3}\", \"__page__\": 0, \"max\": \"\\\"False\\\"\", \"notrunc\": \"\\\"False\\\"\", \"mid\": \"\\\"False\\\"\", \"seqdb\": \"null\", \"toponly\": \"\\\"False\\\"\", \"cm_opts\": \"{\\\"database\\\": null, \\\"__current_case__\\\": 0, \\\"cm_opts_selector\\\": \\\"db\\\"}\", \"reporting_thresholds_opts\": \"{\\\"reporting_thresholds_selector\\\": \\\"\\\", \\\"__current_case__\\\": 3}\", \"cyk\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null}", 515 "changeset_revision": "477d829d3250",
360 "tool_version": "1.1.0.2", 516 "name": "infernal",
361 "type": "tool", 517 "owner": "bgruening",
362 "user_outputs": [] 518 "tool_shed": "toolshed.g2.bx.psu.edu"
363 }, 519 },
364 "7": { 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\\\"\"}",
365 "annotation": "", 521 "tool_version": "1.1.2.0",
366 "id": 7, 522 "type": "tool",
523 "uuid": "842f09a0-b91c-4a9b-a3a5-019f0fda1aba",
524 "workflow_outputs": []
525 },
526 "8": {
527 "annotation": "",
528 "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
529 "errors": null,
530 "id": 8,
367 "input_connections": { 531 "input_connections": {
368 "tool_mode|clusters_bed": { 532 "tool_mode|clusters_bed": {
369 "id": 4, 533 "id": 5,
370 "output_name": "clusters" 534 "output_name": "clusters"
371 }, 535 },
372 "tool_mode|cmsearch_out": { 536 "tool_mode|cmsearch_out": {
373 "id": 6, 537 "id": 7,
374 "output_name": "outfile" 538 "output_name": "outfile"
375 }, 539 },
376 "tool_mode|sim_tab_in": { 540 "tool_mode|sim_tab_in": {
377 "id": 4, 541 "id": 5,
378 "output_name": "sim_tab_out" 542 "output_name": "sim_tab_out"
379 } 543 }
380 }, 544 },
381 "inputs": [], 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,
382 "name": "BlockClust", 560 "name": "BlockClust",
383 "outputs": [ 561 "outputs": [
384 { 562 {
385 "name": "tags_bed", 563 "name": "tags_bed",
386 "type": "bed" 564 "type": "bed"
413 "name": "cluster_hclust", 591 "name": "cluster_hclust",
414 "type": "pdf" 592 "type": "pdf"
415 } 593 }
416 ], 594 ],
417 "position": { 595 "position": {
418 "left": 2049, 596 "left": 2639,
419 "top": 433 597 "top": 338
420 }, 598 },
421 "post_job_actions": { 599 "post_job_actions": {
422 "HideDatasetActionclusters": { 600 "HideDatasetActionclusters": {
423 "action_arguments": {}, 601 "action_arguments": {},
424 "action_type": "HideDatasetAction", 602 "action_type": "HideDatasetAction",
448 "action_arguments": {}, 626 "action_arguments": {},
449 "action_type": "HideDatasetAction", 627 "action_type": "HideDatasetAction",
450 "output_name": "tags_bed" 628 "output_name": "tags_bed"
451 } 629 }
452 }, 630 },
453 "tool_errors": null, 631 "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
454 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", 632 "tool_shed_repository": {
455 "tool_state": "{\"tool_mode\": \"{\\\"cmsearch_out\\\": null, \\\"operation\\\": \\\"post\\\", \\\"clusters_bed\\\": null, \\\"__current_case__\\\": 2, \\\"sim_tab_in\\\": null}\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"cmsearch_out\\\": null, \\\"operation\\\": \\\"post\\\", \\\"clusters_bed\\\": null, \\\"__current_case__\\\": 2, \\\"sim_tab_in\\\": null}\", \"__page__\": 0}", 633 "changeset_revision": "aab6cf87b40a",
456 "tool_version": "1.0.0", 634 "name": "blockclust",
457 "type": "tool", 635 "owner": "rnateam",
458 "user_outputs": [] 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",
640 "type": "tool",
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 ]
459 } 654 }
460 } 655 },
656 "tags": [],
657 "uuid": "a60be50d-44e1-4fb5-90a0-3b849ceaf3e3"
461 } 658 }