comparison Galaxy-Workflow-_jb2testWF_mar26.ga @ 62:ab0d6782a95f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
author fubar
date Thu, 28 Mar 2024 04:51:06 +0000
parents
children
comparison
equal deleted inserted replaced
61:e7a6f7a7148d 62:ab0d6782a95f
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "comments": [],
5 "format-version": "0.1",
6 "name": "'jb2testWF_mar26",
7 "steps": {
8 "0": {
9 "annotation": "",
10 "content_id": null,
11 "errors": null,
12 "id": 0,
13 "input_connections": {},
14 "inputs": [
15 {
16 "description": "",
17 "name": "Merlin"
18 }
19 ],
20 "label": "Merlin",
21 "name": "Input dataset",
22 "outputs": [],
23 "position": {
24 "left": 0,
25 "top": 0
26 },
27 "tool_id": null,
28 "tool_state": "{\"optional\": false, \"tag\": null}",
29 "tool_version": null,
30 "type": "data_input",
31 "uuid": "60c939a2-b9c9-47cd-9ef4-6415e87a1680",
32 "when": null,
33 "workflow_outputs": []
34 },
35 "1": {
36 "annotation": "",
37 "content_id": null,
38 "errors": null,
39 "id": 1,
40 "input_connections": {},
41 "inputs": [
42 {
43 "description": "",
44 "name": "merlin.bw"
45 }
46 ],
47 "label": "merlin.bw",
48 "name": "Input dataset",
49 "outputs": [],
50 "position": {
51 "left": 0,
52 "top": 102
53 },
54 "tool_id": null,
55 "tool_state": "{\"optional\": false, \"tag\": null}",
56 "tool_version": null,
57 "type": "data_input",
58 "uuid": "97251b21-c6c4-4ef9-b985-0cf90f1d2f75",
59 "when": null,
60 "workflow_outputs": []
61 },
62 "2": {
63 "annotation": "",
64 "content_id": null,
65 "errors": null,
66 "id": 2,
67 "input_connections": {},
68 "inputs": [
69 {
70 "description": "",
71 "name": "merlinlastz.maf"
72 }
73 ],
74 "label": "merlinlastz.maf",
75 "name": "Input dataset",
76 "outputs": [],
77 "position": {
78 "left": 0,
79 "top": 204
80 },
81 "tool_id": null,
82 "tool_state": "{\"optional\": false, \"tag\": null}",
83 "tool_version": null,
84 "type": "data_input",
85 "uuid": "41961b03-3ea3-4fe4-a45e-85e2f74b8a48",
86 "when": null,
87 "workflow_outputs": []
88 },
89 "3": {
90 "annotation": "",
91 "content_id": null,
92 "errors": null,
93 "id": 3,
94 "input_connections": {},
95 "inputs": [
96 {
97 "description": "",
98 "name": "merlinblast.xml"
99 }
100 ],
101 "label": "merlinblast.xml",
102 "name": "Input dataset",
103 "outputs": [],
104 "position": {
105 "left": 0,
106 "top": 327
107 },
108 "tool_id": null,
109 "tool_state": "{\"optional\": false, \"tag\": null}",
110 "tool_version": null,
111 "type": "data_input",
112 "uuid": "544106a0-44ea-40c9-8c55-ff5100110ae2",
113 "when": null,
114 "workflow_outputs": []
115 },
116 "4": {
117 "annotation": "",
118 "content_id": null,
119 "errors": null,
120 "id": 4,
121 "input_connections": {},
122 "inputs": [
123 {
124 "description": "",
125 "name": "merlin-sample.bam"
126 }
127 ],
128 "label": "merlin-sample.bam",
129 "name": "Input dataset",
130 "outputs": [],
131 "position": {
132 "left": 0,
133 "top": 450
134 },
135 "tool_id": null,
136 "tool_state": "{\"optional\": false, \"tag\": null}",
137 "tool_version": null,
138 "type": "data_input",
139 "uuid": "42903332-fc6b-4565-b289-22233e6f129a",
140 "when": null,
141 "workflow_outputs": []
142 },
143 "5": {
144 "annotation": "",
145 "content_id": null,
146 "errors": null,
147 "id": 5,
148 "input_connections": {},
149 "inputs": [
150 {
151 "description": "",
152 "name": "merlincram"
153 }
154 ],
155 "label": "merlincram",
156 "name": "Input dataset",
157 "outputs": [],
158 "position": {
159 "left": 0,
160 "top": 573
161 },
162 "tool_id": null,
163 "tool_state": "{\"optional\": false, \"tag\": null}",
164 "tool_version": null,
165 "type": "data_input",
166 "uuid": "54692cdf-d0f6-4631-bfbd-8d71e15003a0",
167 "when": null,
168 "workflow_outputs": []
169 },
170 "6": {
171 "annotation": "",
172 "content_id": null,
173 "errors": null,
174 "id": 6,
175 "input_connections": {},
176 "inputs": [
177 {
178 "description": "",
179 "name": "merlin.gff3"
180 }
181 ],
182 "label": "merlin.gff3",
183 "name": "Input dataset",
184 "outputs": [],
185 "position": {
186 "left": 0,
187 "top": 696
188 },
189 "tool_id": null,
190 "tool_state": "{\"optional\": false, \"tag\": null}",
191 "tool_version": null,
192 "type": "data_input",
193 "uuid": "a84e95f1-d702-4775-b9e7-abd641122be6",
194 "when": null,
195 "workflow_outputs": []
196 },
197 "7": {
198 "annotation": "",
199 "content_id": null,
200 "errors": null,
201 "id": 7,
202 "input_connections": {},
203 "inputs": [
204 {
205 "description": "",
206 "name": "test-6.bed"
207 }
208 ],
209 "label": "test-6.bed",
210 "name": "Input dataset",
211 "outputs": [],
212 "position": {
213 "left": 0,
214 "top": 798
215 },
216 "tool_id": null,
217 "tool_state": "{\"optional\": false, \"tag\": null}",
218 "tool_version": null,
219 "type": "data_input",
220 "uuid": "3306709f-18b5-47b1-86a5-dbf6415254e5",
221 "when": null,
222 "workflow_outputs": []
223 },
224 "8": {
225 "annotation": "",
226 "content_id": null,
227 "errors": null,
228 "id": 8,
229 "input_connections": {},
230 "inputs": [
231 {
232 "description": "",
233 "name": "merlin.vcf"
234 }
235 ],
236 "label": "merlin.vcf",
237 "name": "Input dataset",
238 "outputs": [],
239 "position": {
240 "left": 0,
241 "top": 900
242 },
243 "tool_id": null,
244 "tool_state": "{\"optional\": false, \"tag\": null}",
245 "tool_version": null,
246 "type": "data_input",
247 "uuid": "7f0efd91-8d58-443f-b514-2c9c53ca0074",
248 "when": null,
249 "workflow_outputs": []
250 },
251 "9": {
252 "annotation": "",
253 "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/2.10.1+galaxy2_7",
254 "errors": null,
255 "id": 9,
256 "input_connections": {
257 "reference_genome|genome": {
258 "id": 0,
259 "output_name": "output"
260 },
261 "track_groups_0|data_tracks_0|data_format|useuri|annotation": {
262 "id": 1,
263 "output_name": "output"
264 },
265 "track_groups_0|data_tracks_1|data_format|useuri|annotation": {
266 "id": 2,
267 "output_name": "output"
268 },
269 "track_groups_0|data_tracks_2|data_format|useuri|annotation": {
270 "id": 3,
271 "output_name": "output"
272 },
273 "track_groups_1|data_tracks_0|data_format|useuri|annotation": {
274 "id": 4,
275 "output_name": "output"
276 },
277 "track_groups_1|data_tracks_1|data_format|useuri|annotation": {
278 "id": 5,
279 "output_name": "output"
280 },
281 "track_groups_2|data_tracks_0|data_format|useuri|annotation": {
282 "id": 6,
283 "output_name": "output"
284 },
285 "track_groups_2|data_tracks_1|data_format|useuri|annotation": {
286 "id": 7,
287 "output_name": "output"
288 },
289 "track_groups_2|data_tracks_2|data_format|useuri|annotation": {
290 "id": 8,
291 "output_name": "output"
292 }
293 },
294 "inputs": [
295 {
296 "description": "runtime parameter for tool jbrowse2",
297 "name": "reference_genome"
298 }
299 ],
300 "label": null,
301 "name": "jbrowse2",
302 "outputs": [
303 {
304 "name": "output",
305 "type": "html"
306 }
307 ],
308 "position": {
309 "left": 310,
310 "top": 229
311 },
312 "post_job_actions": {},
313 "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/2.10.1+galaxy2_7",
314 "tool_shed_repository": {
315 "changeset_revision": "81d535970196",
316 "name": "jbrowse2",
317 "owner": "fubar",
318 "tool_shed": "toolshed.g2.bx.psu.edu"
319 },
320 "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"0275163beb0c11eeb2f5934cf82eac23\", \"chromInfo\": \"/mnt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"jbgen\": {\"ucol\": {\"formcoll\": \"form\", \"__current_case__\": 1}, \"zipOut\": false, \"defaultLocation\": \"\", \"session_name\": \"New session\", \"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"track_groups\": [{\"__index__\": 0, \"category\": \"one\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"bigwig\", \"__current_case__\": 7, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"maf\", \"__current_case__\": 6, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 1, \"show_labels\": false, \"show_descriptions\": false, \"display_mode\": \"normal\", \"max_height\": \"600\", \"label\": \"jexl:get(feature,'name') || get(feature,'id')\", \"description\": \"jexl:get(feature,'note') || get(feature,'description')\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 2, \"data_format\": {\"data_format_select\": \"blastxml\", \"__current_case__\": 0, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"blast_parent\": null, \"min_gap\": \"10\", \"is_protein\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 1, \"show_labels\": false, \"show_descriptions\": false, \"display_mode\": \"normal\", \"max_height\": \"600\", \"label\": \"jexl:get(feature,'name') || get(feature,'id')\", \"description\": \"jexl:get(feature,'note') || get(feature,'description')\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"two\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"bam\", \"__current_case__\": 3, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"cram\", \"__current_case__\": 5, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"three\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gff\", \"__current_case__\": 2, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 1, \"show_labels\": false, \"show_descriptions\": false, \"display_mode\": \"normal\", \"max_height\": \"600\", \"label\": \"jexl:get(feature,'name') || get(feature,'id')\", \"description\": \"jexl:get(feature,'note') || get(feature,'description')\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"bed\", \"__current_case__\": 4, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 1, \"show_labels\": false, \"show_descriptions\": false, \"display_mode\": \"normal\", \"max_height\": \"600\", \"label\": \"jexl:get(feature,'name') || get(feature,'id')\", \"description\": \"jexl:get(feature,'note') || get(feature,'description')\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 2, \"data_format\": {\"data_format_select\": \"vcf\", \"__current_case__\": 1, \"useuri\": {\"insource\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearVariantDisplay\", \"__current_case__\": 0, \"show_labels\": false, \"show_descriptions\": false, \"display_mode\": \"normal\", \"max_height\": \"600\"}}, \"track_visibility\": \"default_on\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
321 "tool_version": "2.10.1+galaxy2_7",
322 "type": "tool",
323 "uuid": "ab05b81c-a0a2-4dcc-b76a-e47b15ebcdb9",
324 "when": null,
325 "workflow_outputs": []
326 }
327 },
328 "tags": [],
329 "uuid": "ea921c36-b1bb-4d82-9d35-5965daa3d3b2",
330 "version": 1
331 }