annotate Merge_BAM.ga @ 0:5703e64e15e9 draft default tip

Initial upload
author stemcellcommons
date Tue, 05 Dec 2017 14:58:39 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
1 {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
2 "a_galaxy_workflow": "true",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
3 "annotation": "{\n \"description\": \"Merge a list of BAM files into a single BAM.\",\n \"file_relationship\": {\n \"file_relationship\": {},\n \"value_type\": \"LIST\",\n \"name\": \"List of BAM Files\",\n \"input_files\": [\n {\n \"allowed_filetypes\": [{\"name\": \"BAM\"}],\n \"name\": \"Input File\",\n \"description\": \"File to be merged\"\n }\n ]\n }\n}",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
4 "format-version": "0.1",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
5 "name": "Merge BAM",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
6 "steps": {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
7 "0": {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
8 "annotation": "",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
9 "content_id": null,
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
10 "id": 0,
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
11 "input_connections": {},
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
12 "inputs": [
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
13 {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
14 "description": "",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
15 "name": "Input Dataset Collection"
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
16 }
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
17 ],
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
18 "label": null,
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
19 "name": "Input dataset collection",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
20 "outputs": [],
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
21 "position": {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
22 "left": 200.5,
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
23 "top": 284.5
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
24 },
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
25 "tool_errors": null,
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
26 "tool_id": null,
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
27 "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
28 "tool_version": null,
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
29 "type": "data_collection_input",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
30 "uuid": "d9e52442-15c8-45ba-a07e-fdf9de76ac43",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
31 "workflow_outputs": [
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
32 {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
33 "label": null,
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
34 "output_name": "output",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
35 "uuid": "463f98ce-580f-4a70-8d89-1be510478bb9"
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
36 }
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
37 ]
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
38 },
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
39 "1": {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
40 "annotation": "",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
41 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/1.126.0",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
42 "id": 1,
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
43 "input_connections": {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
44 "inputFile": {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
45 "id": 0,
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
46 "output_name": "output"
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
47 }
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
48 },
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
49 "inputs": [],
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
50 "label": null,
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
51 "name": "MergeSamFiles",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
52 "outputs": [
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
53 {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
54 "name": "outFile",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
55 "type": "bam"
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
56 }
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
57 ],
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
58 "position": {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
59 "left": 575,
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
60 "top": 285
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
61 },
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
62 "post_job_actions": {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
63 "RenameDatasetActionoutFile": {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
64 "action_arguments": {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
65 "newname": "merged"
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
66 },
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
67 "action_type": "RenameDatasetAction",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
68 "output_name": "outFile"
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
69 }
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
70 },
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
71 "tool_errors": null,
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
72 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/1.126.0",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
73 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"merge_sequence_dictionaries\": \"\\\"False\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\", \"inputFile\": \"null\"}",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
74 "tool_version": "1.126.0",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
75 "type": "tool",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
76 "uuid": "0f22ffbb-d375-4d1f-9b53-0abce7390f66",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
77 "workflow_outputs": [
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
78 {
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
79 "label": null,
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
80 "output_name": "outFile",
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
81 "uuid": "82e3ef46-e532-4e2f-bafb-f0875211282f"
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
82 }
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
83 ]
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
84 }
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
85 },
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
86 "uuid": "a920711d-9852-4048-9694-eda710a7513a"
5703e64e15e9 Initial upload
stemcellcommons
parents:
diff changeset
87 }