Mercurial > repos > stemcellcommons > fastqc_workflow

comparison FastQC.ga @ 5:c5784ddcda07 draft default tip

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Update annotations
author stemcellcommons
date Tue, 24 Oct 2017 12:39:37 -0400
parents df2d7e8eacda
children
comparison
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4:0a916a65890f 5:c5784ddcda07
1 { 1 {
2 "a_galaxy_workflow": "true", 2 "a_galaxy_workflow": "true",
3 "annotation": "{\"refinery_type\": \"analysis\"}", 3 "annotation": "{\n \"description\": \"Check for any data quality issues before running analysis workflows.\",\n \"file_relationship\": {\n \"file_relationship\": {},\n \"value_type\": \"LIST\",\n \"name\": \"List of FASTQ Files\",\n \"input_files\": [\n {\n \"allowed_filetypes\": [{\"name\": \"FASTQ\"},{\"name\": \"BAM\"},{\"name\": \"SAM\"}],\n \"name\": \"Input File\",\n \"description\": \"File to run QC on\"\n }\n ]\n }\n}",
4 "format-version": "0.1", 4 "format-version": "0.1",
5 "name": "FastQC", 5 "name": "FastQC",
6 "steps": { 6 "steps": {
7 "0": { 7 "0": {
8 "annotation": "", 8 "annotation": "",
9 "content_id": null,
9 "id": 0, 10 "id": 0,
10 "input_connections": {}, 11 "input_connections": {},
11 "inputs": [ 12 "inputs": [
12 { 13 {
13 "description": "", 14 "description": "",
14 "name": "Input Dataset" 15 "name": "Input Dataset"
15 } 16 }
16 ], 17 ],
18 "label": null,
17 "name": "Input dataset", 19 "name": "Input dataset",
18 "outputs": [], 20 "outputs": [],
19 "position": { 21 "position": {
20 "left": 155, 22 "left": 315,
21 "top": 389 23 "top": 410
22 }, 24 },
23 "tool_errors": null, 25 "tool_errors": null,
24 "tool_id": null, 26 "tool_id": null,
25 "tool_state": "{\"name\": \"Input Dataset\"}", 27 "tool_state": "{\"name\": \"Input Dataset\"}",
26 "tool_version": null, 28 "tool_version": null,
27 "type": "data_input", 29 "type": "data_input",
28 "user_outputs": [] 30 "uuid": "983e8aa7-72ca-446a-95a4-dc5f645421ec",
31 "workflow_outputs": [
32 {
33 "label": null,
34 "output_name": "output",
35 "uuid": "77b252a2-567b-4e1c-b5d1-41b8027ecca4"
36 }
37 ]
29 }, 38 },
30 "1": { 39 "1": {
31 "annotation": "{\"html_file\": {\"name\": \"fastqc_report\", \"description\": \"HTML file containing FASTQC report.\", \"type\": \"html\"}, \"text_file\": {\"name\": \"fastqc_results\", \"description\": \"Data file containing FASTQC results.\", \"type\": \"txt\"}}", 40 "annotation": "{\"html_file\": {\"name\": \"fastqc_report\", \"description\": \"HTML file containing FASTQC report.\", \"type\": \"html\"}, \"text_file\": {\"name\": \"fastqc_results\", \"description\": \"Data file containing FASTQC results.\", \"type\": \"txt\"}}",
41 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65",
32 "id": 1, 42 "id": 1,
33 "input_connections": { 43 "input_connections": {
34 "input_file": { 44 "input_file": {
35 "id": 0, 45 "id": 0,
36 "output_name": "output" 46 "output_name": "output"
37 } 47 }
38 }, 48 },
39 "inputs": [], 49 "inputs": [],
50 "label": null,
40 "name": "FastQC", 51 "name": "FastQC",
41 "outputs": [ 52 "outputs": [
42 { 53 {
43 "name": "html_file", 54 "name": "html_file",
44 "type": "html" 55 "type": "html"
47 "name": "text_file", 58 "name": "text_file",
48 "type": "txt" 59 "type": "txt"
49 } 60 }
50 ], 61 ],
51 "position": { 62 "position": {
52 "left": 439, 63 "left": 599,
53 "top": 330.5 64 "top": 351.5
54 }, 65 },
55 "post_job_actions": {}, 66 "post_job_actions": {
67 "RenameDatasetActionhtml_file": {
68 "action_arguments": {
69 "newname": "fastqc_report"
70 },
71 "action_type": "RenameDatasetAction",
72 "output_name": "html_file"
73 },
74 "RenameDatasetActiontext_file": {
75 "action_arguments": {
76 "newname": "fastqc_results"
77 },
78 "action_type": "RenameDatasetAction",
79 "output_name": "text_file"
80 }
81 },
56 "tool_errors": null, 82 "tool_errors": null,
57 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65", 83 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65",
58 "tool_state": "{\"__page__\": 0, \"contaminants\": \"null\", \"__rerun_remap_job_id__\": null, \"limits\": \"null\", \"input_file\": \"null\"}", 84 "tool_state": "{\"__page__\": 0, \"contaminants\": \"null\", \"__rerun_remap_job_id__\": null, \"limits\": \"null\", \"input_file\": \"null\"}",
59 "tool_version": "0.65", 85 "tool_version": "0.65",
60 "type": "tool", 86 "type": "tool",
61 "user_outputs": [] 87 "uuid": "88cc0f74-d5ad-421b-9330-d3ff49c79bb0",
88 "workflow_outputs": [
89 {
90 "label": null,
91 "output_name": "html_file",
92 "uuid": "91f9c648-5ddc-495f-b3dd-f043c9af0862"
93 },
94 {
95 "label": null,
96 "output_name": "text_file",
97 "uuid": "dcbdf17b-0c13-4418-b255-1cf411312b74"
98 }
99 ]
62 } 100 }
63 } 101 },
102 "uuid": "4f81b632-d3cd-460f-9b3c-62593b41dfab"
64 } 103 }