Mercurial > repos > bgruening > deeptools_workflows
comparison Compute_and_correct_GC_bias.ga @ 0:16fc7f46ee23 draft default tip
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author | bgruening |
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date | Thu, 03 Apr 2014 11:11:15 -0400 |
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-1:000000000000 | 0:16fc7f46ee23 |
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1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "", | |
4 "format-version": "0.1", | |
5 "name": "Compute and correct GC bias", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "", | |
9 "id": 0, | |
10 "input_connections": {}, | |
11 "inputs": [ | |
12 { | |
13 "description": "", | |
14 "name": "BAM file to be checked for GC bias" | |
15 } | |
16 ], | |
17 "name": "Input dataset", | |
18 "outputs": [], | |
19 "position": { | |
20 "left": 148, | |
21 "top": 505.88330078125 | |
22 }, | |
23 "tool_errors": null, | |
24 "tool_id": null, | |
25 "tool_state": "{\"name\": \"BAM file to be checked for GC bias\"}", | |
26 "tool_version": null, | |
27 "type": "data_input", | |
28 "user_outputs": [] | |
29 }, | |
30 "1": { | |
31 "annotation": "", | |
32 "id": 1, | |
33 "input_connections": { | |
34 "bamInput": { | |
35 "id": 0, | |
36 "output_name": "output" | |
37 } | |
38 }, | |
39 "inputs": [ | |
40 { | |
41 "description": "runtime parameter for tool computeGCBias", | |
42 "name": "region" | |
43 }, | |
44 { | |
45 "description": "runtime parameter for tool computeGCBias", | |
46 "name": "source" | |
47 }, | |
48 { | |
49 "description": "runtime parameter for tool computeGCBias", | |
50 "name": "effectiveGenomeSize" | |
51 }, | |
52 { | |
53 "description": "runtime parameter for tool computeGCBias", | |
54 "name": "image_format" | |
55 }, | |
56 { | |
57 "description": "runtime parameter for tool computeGCBias", | |
58 "name": "fragmentLength" | |
59 } | |
60 ], | |
61 "name": "computeGCBias", | |
62 "outputs": [ | |
63 { | |
64 "name": "outFileName", | |
65 "type": "tabular" | |
66 }, | |
67 { | |
68 "name": "outImageName", | |
69 "type": "png" | |
70 } | |
71 ], | |
72 "position": { | |
73 "left": 404.61669921875, | |
74 "top": 200 | |
75 }, | |
76 "post_job_actions": { | |
77 "HideDatasetActionoutFileName": { | |
78 "action_arguments": {}, | |
79 "action_type": "HideDatasetAction", | |
80 "output_name": "outFileName" | |
81 } | |
82 }, | |
83 "tool_errors": null, | |
84 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeGCBias/1.1.0", | |
85 "tool_state": "{\"__page__\": 0, \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bamInput\": \"null\", \"source\": \"{\\\"input1_2bit\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"ref_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"effectiveGenomeSize\": \"{\\\"effectiveGenomeSize_opt\\\": \\\"specific\\\", \\\"effectiveGenomeSize\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"advancedOpt\": \"{\\\"filterOut\\\": null, \\\"extraSampling\\\": null, \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"sampleSize\\\": \\\"50000000\\\", \\\"__current_case__\\\": 1, \\\"regionSize\\\": \\\"300\\\"}\", \"image_format\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fragmentLength\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", | |
86 "tool_version": "1.1.0", | |
87 "type": "tool", | |
88 "user_outputs": [] | |
89 }, | |
90 "2": { | |
91 "annotation": "", | |
92 "id": 2, | |
93 "input_connections": { | |
94 "GCbiasFrequenciesFile": { | |
95 "id": 1, | |
96 "output_name": "outFileName" | |
97 }, | |
98 "bamInput": { | |
99 "id": 0, | |
100 "output_name": "output" | |
101 } | |
102 }, | |
103 "inputs": [ | |
104 { | |
105 "description": "runtime parameter for tool correctGCBias", | |
106 "name": "region" | |
107 }, | |
108 { | |
109 "description": "runtime parameter for tool correctGCBias", | |
110 "name": "source" | |
111 }, | |
112 { | |
113 "description": "runtime parameter for tool correctGCBias", | |
114 "name": "effectiveGenomeSize" | |
115 } | |
116 ], | |
117 "name": "correctGCBias", | |
118 "outputs": [ | |
119 { | |
120 "name": "outFileName", | |
121 "type": "bam" | |
122 } | |
123 ], | |
124 "position": { | |
125 "left": 734.61669921875, | |
126 "top": 462 | |
127 }, | |
128 "post_job_actions": { | |
129 "RenameDatasetActionoutFileName": { | |
130 "action_arguments": { | |
131 "newname": "GCcorrected BAM file" | |
132 }, | |
133 "action_type": "RenameDatasetAction", | |
134 "output_name": "outFileName" | |
135 } | |
136 }, | |
137 "tool_errors": null, | |
138 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_correctGCBias/1.1.0", | |
139 "tool_state": "{\"__page__\": 0, \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bamInput\": \"null\", \"source\": \"{\\\"input1_2bit\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"ref_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"effectiveGenomeSize\": \"{\\\"effectiveGenomeSize_opt\\\": \\\"specific\\\", \\\"effectiveGenomeSize\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"GCbiasFrequenciesFile\": \"null\", \"advancedOpt\": \"{\\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"binSize\\\": \\\"50\\\"}\", \"__rerun_remap_job_id__\": null}", | |
140 "tool_version": "1.1.0", | |
141 "type": "tool", | |
142 "user_outputs": [] | |
143 } | |
144 } | |
145 } |