Mercurial > repos > rnateam > blockclust_workflow

comparison blockclust_workflow_clustering.ga @ 1:25afbac62e0d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author rnateam
date Wed, 07 May 2014 04:59:28 -0400
parents
children 59e321cafca7
comparison
equal deleted inserted replaced
0:b2040467dad2 1:25afbac62e0d
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "Until clustering step. No post processing included.",
4 "format-version": "0.1",
5 "name": "BlockClustWorkflow_clustering",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "",
14 "name": "Input BAM file"
15 }
16 ],
17 "name": "Input dataset",
18 "outputs": [],
19 "position": {
20 "left": 217,
21 "top": 282.5
22 },
23 "tool_errors": null,
24 "tool_id": null,
25 "tool_state": "{\"name\": \"Input BAM file\"}",
26 "tool_version": null,
27 "type": "data_input",
28 "user_outputs": []
29 },
30 "1": {
31 "annotation": "",
32 "id": 1,
33 "input_connections": {
34 "tool_mode|reads_bam": {
35 "id": 0,
36 "output_name": "output"
37 }
38 },
39 "inputs": [],
40 "name": "BlockClust",
41 "outputs": [
42 {
43 "name": "tags_bed",
44 "type": "bed"
45 },
46 {
47 "name": "hclust_plot",
48 "type": "pdf"
49 },
50 {
51 "name": "clusters",
52 "type": "bed"
53 },
54 {
55 "name": "model_based_pred_bed",
56 "type": "bed"
57 },
58 {
59 "name": "nearest_neighbour_pred_bed",
60 "type": "bed"
61 },
62 {
63 "name": "sim_tab_out",
64 "type": "tabular"
65 },
66 {
67 "name": "cluster_dist",
68 "type": "pdf"
69 },
70 {
71 "name": "cluster_hclust",
72 "type": "pdf"
73 }
74 ],
75 "position": {
76 "left": 446.5,
77 "top": 239.5
78 },
79 "post_job_actions": {
80 "HideDatasetActioncluster_dist": {
81 "action_arguments": {},
82 "action_type": "HideDatasetAction",
83 "output_name": "cluster_dist"
84 },
85 "HideDatasetActioncluster_hclust": {
86 "action_arguments": {},
87 "action_type": "HideDatasetAction",
88 "output_name": "cluster_hclust"
89 },
90 "HideDatasetActionclusters": {
91 "action_arguments": {},
92 "action_type": "HideDatasetAction",
93 "output_name": "clusters"
94 },
95 "HideDatasetActionhclust_plot": {
96 "action_arguments": {},
97 "action_type": "HideDatasetAction",
98 "output_name": "hclust_plot"
99 },
100 "HideDatasetActionmodel_based_pred_bed": {
101 "action_arguments": {},
102 "action_type": "HideDatasetAction",
103 "output_name": "model_based_pred_bed"
104 },
105 "HideDatasetActionnearest_neighbour_pred_bed": {
106 "action_arguments": {},
107 "action_type": "HideDatasetAction",
108 "output_name": "nearest_neighbour_pred_bed"
109 },
110 "HideDatasetActionsim_tab_out": {
111 "action_arguments": {},
112 "action_type": "HideDatasetAction",
113 "output_name": "sim_tab_out"
114 },
115 "HideDatasetActiontags_bed": {
116 "action_arguments": {},
117 "action_type": "HideDatasetAction",
118 "output_name": "tags_bed"
119 }
120 },
121 "tool_errors": null,
122 "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0",
123 "tool_state": "{\"tool_mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
124 "tool_version": "1.0.0",
125 "type": "tool",
126 "user_outputs": []
127 },
128 "2": {
129 "annotation": "",
130 "id": 2,
131 "input_connections": {
132 "input": {
133 "id": 1,
134 "output_name": "tags_bed"
135 }
136 },
137 "inputs": [],
138 "name": "Sort",
139 "outputs": [
140 {
141 "name": "out_file1",
142 "type": "input"
143 }
144 ],
145 "position": {
146 "left": 740,
147 "top": 271
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",
174 "outputs": [
175 {
176 "name": "output",
177 "type": "tabular"
178 }
179 ],
180 "position": {
181 "left": 961.5,
182 "top": 219.5
183 },
184 "post_job_actions": {
185 "HideDatasetActionoutput": {
186 "action_arguments": {},
187 "action_type": "HideDatasetAction",
188 "output_name": "output"
189 }
190 },
191 "tool_errors": null,
192 "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1",
193 "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\\\"\"}",
194 "tool_version": "0.1",
195 "type": "tool",
196 "user_outputs": []
197 },
198 "4": {
199 "annotation": "",
200 "id": 4,
201 "input_connections": {
202 "tool_mode|input_bbo": {
203 "id": 3,
204 "output_name": "output"
205 }
206 },
207 "inputs": [
208 {
209 "description": "runtime parameter for tool BlockClust",
210 "name": "tool_mode"
211 }
212 ],
213 "name": "BlockClust",
214 "outputs": [
215 {
216 "name": "tags_bed",
217 "type": "bed"
218 },
219 {
220 "name": "hclust_plot",
221 "type": "pdf"
222 },
223 {
224 "name": "clusters",
225 "type": "bed"
226 },
227 {
228 "name": "model_based_pred_bed",
229 "type": "bed"
230 },
231 {
232 "name": "nearest_neighbour_pred_bed",
233 "type": "bed"
234 },
235 {
236 "name": "sim_tab_out",
237 "type": "tabular"
238 },
239 {
240 "name": "cluster_dist",
241 "type": "pdf"
242 },
243 {
244 "name": "cluster_hclust",
245 "type": "pdf"
246 }
247 ],
248 "position": {
249 "left": 1220.5,
250 "top": 375.5
251 },
252 "post_job_actions": {
253 "HideDatasetActioncluster_dist": {
254 "action_arguments": {},
255 "action_type": "HideDatasetAction",
256 "output_name": "cluster_dist"
257 },
258 "HideDatasetActioncluster_hclust": {
259 "action_arguments": {},
260 "action_type": "HideDatasetAction",
261 "output_name": "cluster_hclust"
262 },
263 "HideDatasetActionsim_tab_out": {
264 "action_arguments": {},
265 "action_type": "HideDatasetAction",
266 "output_name": "sim_tab_out"
267 },
268 "HideDatasetActiontags_bed": {
269 "action_arguments": {},
270 "action_type": "HideDatasetAction",
271 "output_name": "tags_bed"
272 }
273 },
274 "tool_errors": null,
275 "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0",
276 "tool_state": "{\"tool_mode\": \"{\\\"pred\\\": {\\\"pred_mode\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"enable_pred\\\": \\\"yes\\\", \\\"__current_case__\\\": 0}, \\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
277 "tool_version": "1.0.0",
278 "type": "tool",
279 "user_outputs": []
280 }
281 }
282 }