Mercurial > repos > bgruening > deeptools_workflows
comparison Add_chr_to_first_column_of_a_6_columns_BED_file.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": "Add 'chr' to first column of a BED file (must have 6 columns)", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "", | |
9 "id": 0, | |
10 "input_connections": {}, | |
11 "inputs": [ | |
12 { | |
13 "description": "", | |
14 "name": "BED file" | |
15 } | |
16 ], | |
17 "name": "Input dataset", | |
18 "outputs": [], | |
19 "position": { | |
20 "left": 200, | |
21 "top": 193 | |
22 }, | |
23 "tool_errors": null, | |
24 "tool_id": null, | |
25 "tool_state": "{\"name\": \"BED file\"}", | |
26 "tool_version": null, | |
27 "type": "data_input", | |
28 "user_outputs": [] | |
29 }, | |
30 "1": { | |
31 "annotation": "", | |
32 "id": 1, | |
33 "input_connections": { | |
34 "input": { | |
35 "id": 0, | |
36 "output_name": "output" | |
37 } | |
38 }, | |
39 "inputs": [], | |
40 "name": "Add column", | |
41 "outputs": [ | |
42 { | |
43 "name": "out_file1", | |
44 "type": "input" | |
45 } | |
46 ], | |
47 "position": { | |
48 "left": 423, | |
49 "top": 200 | |
50 }, | |
51 "post_job_actions": { | |
52 "HideDatasetActionout_file1": { | |
53 "action_arguments": {}, | |
54 "action_type": "HideDatasetAction", | |
55 "output_name": "out_file1" | |
56 } | |
57 }, | |
58 "tool_errors": null, | |
59 "tool_id": "addValue", | |
60 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"chr\\\"\", \"iterate\": \"\\\"no\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\"}", | |
61 "tool_version": "1.0.0", | |
62 "type": "tool", | |
63 "user_outputs": [] | |
64 }, | |
65 "2": { | |
66 "annotation": "", | |
67 "id": 2, | |
68 "input_connections": { | |
69 "input1": { | |
70 "id": 1, | |
71 "output_name": "out_file1" | |
72 } | |
73 }, | |
74 "inputs": [], | |
75 "name": "Merge Columns", | |
76 "outputs": [ | |
77 { | |
78 "name": "out_file1", | |
79 "type": "tabular" | |
80 } | |
81 ], | |
82 "position": { | |
83 "left": 657, | |
84 "top": 211 | |
85 }, | |
86 "post_job_actions": { | |
87 "HideDatasetActionout_file1": { | |
88 "action_arguments": {}, | |
89 "action_type": "HideDatasetAction", | |
90 "output_name": "out_file1" | |
91 } | |
92 }, | |
93 "tool_errors": null, | |
94 "tool_id": "mergeCols1", | |
95 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"col2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"col1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"7\\\"}\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\", \"columns\": \"[]\"}", | |
96 "tool_version": "1.0.1", | |
97 "type": "tool", | |
98 "user_outputs": [] | |
99 }, | |
100 "3": { | |
101 "annotation": "", | |
102 "id": 3, | |
103 "input_connections": { | |
104 "input": { | |
105 "id": 2, | |
106 "output_name": "out_file1" | |
107 } | |
108 }, | |
109 "inputs": [], | |
110 "name": "Cut", | |
111 "outputs": [ | |
112 { | |
113 "name": "out_file1", | |
114 "type": "tabular" | |
115 } | |
116 ], | |
117 "position": { | |
118 "left": 872, | |
119 "top": 205 | |
120 }, | |
121 "post_job_actions": { | |
122 "ChangeDatatypeActionout_file1": { | |
123 "action_arguments": { | |
124 "newtype": "interval" | |
125 }, | |
126 "action_type": "ChangeDatatypeAction", | |
127 "output_name": "out_file1" | |
128 }, | |
129 "RenameDatasetActionout_file1": { | |
130 "action_arguments": { | |
131 "newname": "added \"chr\" to chromosome name" | |
132 }, | |
133 "action_type": "RenameDatasetAction", | |
134 "output_name": "out_file1" | |
135 } | |
136 }, | |
137 "tool_errors": null, | |
138 "tool_id": "Cut1", | |
139 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c8,c2,c3,c4,c5,c6\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\"}", | |
140 "tool_version": "1.0.2", | |
141 "type": "tool", | |
142 "user_outputs": [] | |
143 } | |
144 } | |
145 } |