comparison Add_chr_to_first_column_of_a_6_columns_BED_file.ga @ 0:16fc7f46ee23 draft default tip

Uploaded
author bgruening
date Thu, 03 Apr 2014 11:11:15 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:16fc7f46ee23
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 }