annotate Galaxy-Workflow-TR_genome_profiling.ga @ 0:07588b899c13 draft

Uploaded
author arkarachai-fungtammasan
date Wed, 01 Apr 2015 17:05:51 -0400
parents
children 29924ae65c45
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
1 {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
2 "a_galaxy_workflow": "true",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
3 "annotation": "",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
4 "format-version": "0.1",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
5 "name": "TR genome profiling",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
6 "steps": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
7 "0": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
8 "annotation": "",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
9 "id": 0,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
10 "input_connections": {},
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
11 "inputs": [
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
12 {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
13 "description": "",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
14 "name": "fasta reference file"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
15 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
16 ],
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
17 "name": "Input dataset",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
18 "outputs": [],
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
19 "position": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
20 "left": 200,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
21 "top": 250
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
22 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
23 "tool_errors": null,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
24 "tool_id": null,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
25 "tool_state": "{\"name\": \"fasta reference file\"}",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
26 "tool_version": null,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
27 "type": "data_input",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
28 "user_outputs": []
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
29 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
30 "1": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
31 "annotation": "",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
32 "id": 1,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
33 "input_connections": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
34 "filePath": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
35 "id": 0,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
36 "output_name": "output"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
37 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
38 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
39 "inputs": [],
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
40 "name": "Microsatellite detection",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
41 "outputs": [
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
42 {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
43 "name": "stdout",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
44 "type": "tabular"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
45 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
46 ],
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
47 "position": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
48 "left": 430,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
49 "top": 250
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
50 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
51 "post_job_actions": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
52 "ChangeDatatypeActionstdout": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
53 "action_arguments": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
54 "newtype": "tabular"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
55 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
56 "action_type": "ChangeDatatypeAction",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
57 "output_name": "stdout"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
58 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
59 "HideDatasetActionstdout": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
60 "action_arguments": {},
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
61 "action_type": "HideDatasetAction",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
62 "output_name": "stdout"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
63 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
64 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
65 "tool_errors": null,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
66 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/microsatellite/1.0.0",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
67 "tool_state": "{\"__page__\": 0, \"flankSetting\": \"{\\\"noflankdisplay\\\": \\\"False\\\", \\\"flankdisplay\\\": \\\"0\\\", \\\"__current_case__\\\": 0}\", \"filePath\": \"null\", \"minlength\": \"\\\"5\\\"\", \"hammingThreshold\": \"\\\"0\\\"\", \"period\": \"\\\"1\\\"\", \"surfix\": \"\\\"0\\\"\", \"prefix\": \"\\\"0\\\"\", \"__rerun_remap_job_id__\": null, \"inputFileSource\": \"{\\\"inputFileType\\\": \\\"fasta\\\", \\\"__current_case__\\\": 2}\", \"partialmotifs\": \"\\\"True\\\"\", \"multipleruns\": \"\\\"True\\\"\"}",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
68 "tool_version": "1.0.0",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
69 "type": "tool",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
70 "user_outputs": []
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
71 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
72 "2": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
73 "annotation": "",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
74 "id": 2,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
75 "input_connections": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
76 "input": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
77 "id": 1,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
78 "output_name": "stdout"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
79 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
80 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
81 "inputs": [],
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
82 "name": "Compute",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
83 "outputs": [
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
84 {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
85 "name": "out_file1",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
86 "type": "input"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
87 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
88 ],
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
89 "position": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
90 "left": 688,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
91 "top": 250
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
92 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
93 "post_job_actions": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
94 "HideDatasetActionout_file1": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
95 "action_arguments": {},
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
96 "action_type": "HideDatasetAction",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
97 "output_name": "out_file1"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
98 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
99 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
100 "tool_errors": null,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
101 "tool_id": "Add_a_column1",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
102 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"int(c1+c2)\\\"\", \"round\": \"\\\"no\\\"\", \"__page__\": 0}",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
103 "tool_version": "1.1.0",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
104 "type": "tool",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
105 "user_outputs": []
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
106 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
107 "3": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
108 "annotation": "",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
109 "id": 3,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
110 "input_connections": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
111 "input": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
112 "id": 2,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
113 "output_name": "out_file1"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
114 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
115 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
116 "inputs": [],
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
117 "name": "Compute",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
118 "outputs": [
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
119 {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
120 "name": "out_file1",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
121 "type": "input"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
122 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
123 ],
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
124 "position": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
125 "left": 916,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
126 "top": 250
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
127 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
128 "post_job_actions": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
129 "HideDatasetActionout_file1": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
130 "action_arguments": {},
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
131 "action_type": "HideDatasetAction",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
132 "output_name": "out_file1"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
133 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
134 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
135 "tool_errors": null,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
136 "tool_id": "Add_a_column1",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
137 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"len(c4)\\\"\", \"round\": \"\\\"no\\\"\", \"__page__\": 0}",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
138 "tool_version": "1.1.0",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
139 "type": "tool",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
140 "user_outputs": []
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
141 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
142 "4": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
143 "annotation": "",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
144 "id": 4,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
145 "input_connections": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
146 "input": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
147 "id": 3,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
148 "output_name": "out_file1"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
149 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
150 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
151 "inputs": [],
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
152 "name": "Cut",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
153 "outputs": [
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
154 {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
155 "name": "out_file1",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
156 "type": "tabular"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
157 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
158 ],
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
159 "position": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
160 "left": 1144,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
161 "top": 250
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
162 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
163 "post_job_actions": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
164 "ChangeDatatypeActionout_file1": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
165 "action_arguments": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
166 "newtype": "interval"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
167 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
168 "action_type": "ChangeDatatypeAction",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
169 "output_name": "out_file1"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
170 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
171 "ColumnSetActionout_file1": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
172 "action_arguments": {
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
173 "chromCol": "1",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
174 "endCol": "3",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
175 "nameCol": "",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
176 "startCol": "2",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
177 "strandCol": ""
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
178 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
179 "action_type": "ColumnSetAction",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
180 "output_name": "out_file1"
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
181 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
182 },
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
183 "tool_errors": null,
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
184 "tool_id": "Cut1",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
185 "tool_state": "{\"columnList\": \"\\\"c6,c2,c9,c4,c1,c10\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
186 "tool_version": "1.0.2",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
187 "type": "tool",
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
188 "user_outputs": []
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
189 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
190 }
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
191 }