Mercurial > repos > stemcellcommons > qualimap_bamqc_workflow

comparison Qualimap_BAM_QC.ga @ 0:064dbe5f3b2f draft default tip

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planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
author scottx611x
date Tue, 04 Sep 2018 13:53:32 -0400
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-1:000000000000 0:064dbe5f3b2f
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "{ \n \"description\": \"Quality control of mapped reads\", \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 run Qualimap BAM QC on\" \n } \n ] \n } \n}",
4 "format-version": "0.1",
5 "name": "Qualimap Bam QC",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "content_id": null,
10 "errors": null,
11 "id": 0,
12 "input_connections": {},
13 "inputs": [],
14 "label": null,
15 "name": "Input dataset",
16 "outputs": [],
17 "position": {
18 "left": 494,
19 "top": 304.5
20 },
21 "tool_id": null,
22 "tool_state": "{}",
23 "tool_version": null,
24 "type": "data_input",
25 "uuid": "354d9a2d-aadd-4c58-886f-5cf9659df944",
26 "workflow_outputs": [
27 {
28 "label": null,
29 "output_name": "output",
30 "uuid": "6e6fd3a9-4d85-4095-9e25-e868020b97f7"
31 }
32 ]
33 },
34 "1": {
35 "annotation": "",
36 "content_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/qualimap2_bamqc/qualimap_bamqc/2.2",
37 "errors": null,
38 "id": 1,
39 "input_connections": {
40 "input_realigned_bam_file": {
41 "id": 0,
42 "output_name": "output"
43 }
44 },
45 "inputs": [
46 {
47 "description": "runtime parameter for tool QualiMap BamQC",
48 "name": "input_realigned_bam_file"
49 }
50 ],
51 "label": null,
52 "name": "QualiMap BamQC",
53 "outputs": [
54 {
55 "name": "genome_results",
56 "type": "txt"
57 },
58 {
59 "name": "raw_data_qualimapReport",
60 "type": "zip"
61 }
62 ],
63 "position": {
64 "left": 872,
65 "top": 359.5
66 },
67 "post_job_actions": {
68 "RenameDatasetActiongenome_results": {
69 "action_arguments": {
70 "newname": "genome_results"
71 },
72 "action_type": "RenameDatasetAction",
73 "output_name": "genome_results"
74 },
75 "RenameDatasetActionraw_data_qualimapReport": {
76 "action_arguments": {
77 "newname": "raw_data_qualimapReport"
78 },
79 "action_type": "RenameDatasetAction",
80 "output_name": "raw_data_qualimapReport"
81 }
82 },
83 "tool_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/qualimap2_bamqc/qualimap_bamqc/2.2",
84 "tool_shed_repository": {
85 "changeset_revision": "a2438e0f1bbf",
86 "name": "qualimap2_bamqc",
87 "owner": "refinery-platform",
88 "tool_shed": "toolshed.g2.bx.psu.edu"
89 },
90 "tool_state": "{\"mem_size\": \"\\\"8G\\\"\", \"__rerun_remap_job_id__\": null, \"input_realigned_bam_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null}",
91 "tool_version": "2.2",
92 "type": "tool",
93 "uuid": "8e63fbd9-22df-4b7b-a0d1-88e8be17bf16",
94 "workflow_outputs": [
95 {
96 "label": null,
97 "output_name": "raw_data_qualimapReport",
98 "uuid": "71d23433-f0ef-452d-9c4b-b4376e2665de"
99 },
100 {
101 "label": null,
102 "output_name": "genome_results",
103 "uuid": "d5f56231-b611-425a-b2e1-d2a9072111f9"
104 }
105 ]
106 }
107 },
108 "uuid": "27bccc25-073c-4061-b573-9cfe9ed47324"
109 }