|
13
|
1 {
|
|
|
2 "a_galaxy_workflow": "true",
|
|
|
3 "annotation": "Compare Methylation levels of 2 samples",
|
|
|
4 "format-version": "0.1",
|
|
|
5 "name": "Differential_Methylation_Bismark",
|
|
|
6 "steps": {
|
|
|
7 "0": {
|
|
|
8 "annotation": "",
|
|
|
9 "id": 0,
|
|
|
10 "input_connections": {},
|
|
|
11 "inputs": [],
|
|
|
12 "name": "Bismark",
|
|
|
13 "outputs": [
|
|
|
14 {
|
|
|
15 "name": "summary",
|
|
|
16 "type": "txt"
|
|
|
17 },
|
|
|
18 {
|
|
|
19 "name": "output",
|
|
|
20 "type": "bam"
|
|
|
21 }
|
|
|
22 ],
|
|
|
23 "position": {
|
|
|
24 "left": 198,
|
|
|
25 "top": 200
|
|
|
26 },
|
|
|
27 "post_job_actions": {},
|
|
|
28 "tool_errors": null,
|
|
|
29 "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/bismark_tool/0.7.6",
|
|
|
30 "tool_state": "{\"__page__\": 0, \"format_option\": \"\\\"fastq\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\", \"option_input\": \"{\\\"input_option\\\": \\\"mates\\\", \\\"file_mate1\\\": null, \\\"__current_case__\\\": 0, \\\"file_mate2\\\": null}\", \"non_directional\": \"\\\"ON\\\"\"}",
|
|
|
31 "tool_version": "0.7.6",
|
|
|
32 "type": "tool",
|
|
|
33 "user_outputs": []
|
|
|
34 },
|
|
|
35 "1": {
|
|
|
36 "annotation": "",
|
|
|
37 "id": 1,
|
|
|
38 "input_connections": {},
|
|
|
39 "inputs": [],
|
|
|
40 "name": "Bismark",
|
|
|
41 "outputs": [
|
|
|
42 {
|
|
|
43 "name": "summary",
|
|
|
44 "type": "txt"
|
|
|
45 },
|
|
|
46 {
|
|
|
47 "name": "output",
|
|
|
48 "type": "bam"
|
|
|
49 }
|
|
|
50 ],
|
|
|
51 "position": {
|
|
|
52 "left": 200,
|
|
|
53 "top": 375
|
|
|
54 },
|
|
|
55 "post_job_actions": {},
|
|
|
56 "tool_errors": null,
|
|
|
57 "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/bismark_tool/0.7.6",
|
|
|
58 "tool_state": "{\"__page__\": 0, \"format_option\": \"\\\"fastq\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\", \"option_input\": \"{\\\"input_option\\\": \\\"mates\\\", \\\"file_mate1\\\": null, \\\"__current_case__\\\": 0, \\\"file_mate2\\\": null}\", \"non_directional\": \"\\\"ON\\\"\"}",
|
|
|
59 "tool_version": "0.7.6",
|
|
|
60 "type": "tool",
|
|
|
61 "user_outputs": []
|
|
|
62 },
|
|
|
63 "2": {
|
|
|
64 "annotation": "",
|
|
|
65 "id": 2,
|
|
|
66 "input_connections": {
|
|
|
67 "bamfile": {
|
|
|
68 "id": 0,
|
|
|
69 "output_name": "output"
|
|
|
70 }
|
|
|
71 },
|
|
|
72 "inputs": [],
|
|
|
73 "name": "Methylation Extractor",
|
|
|
74 "outputs": [
|
|
|
75 {
|
|
|
76 "name": "output",
|
|
|
77 "type": "bedgraph"
|
|
|
78 },
|
|
|
79 {
|
|
|
80 "name": "summary",
|
|
|
81 "type": "txt"
|
|
|
82 }
|
|
|
83 ],
|
|
|
84 "position": {
|
|
|
85 "left": 432.5,
|
|
|
86 "top": 218
|
|
|
87 },
|
|
|
88 "post_job_actions": {},
|
|
|
89 "tool_errors": null,
|
|
|
90 "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/methyation_extractor_tool/0.7.6",
|
|
|
91 "tool_state": "{\"__page__\": 0, \"bamfile\": \"null\", \"ending\": \"\\\"paired\\\"\", \"no_overlap\": \"\\\"ON\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\", \"report\": \"\\\"ON\\\"\"}",
|
|
|
92 "tool_version": "0.7.6",
|
|
|
93 "type": "tool",
|
|
|
94 "user_outputs": []
|
|
|
95 },
|
|
|
96 "3": {
|
|
|
97 "annotation": "",
|
|
|
98 "id": 3,
|
|
|
99 "input_connections": {
|
|
|
100 "bamfile": {
|
|
|
101 "id": 1,
|
|
|
102 "output_name": "output"
|
|
|
103 }
|
|
|
104 },
|
|
|
105 "inputs": [],
|
|
|
106 "name": "Methylation Extractor",
|
|
|
107 "outputs": [
|
|
|
108 {
|
|
|
109 "name": "output",
|
|
|
110 "type": "bedgraph"
|
|
|
111 },
|
|
|
112 {
|
|
|
113 "name": "summary",
|
|
|
114 "type": "txt"
|
|
|
115 }
|
|
|
116 ],
|
|
|
117 "position": {
|
|
|
118 "left": 432.5,
|
|
|
119 "top": 394
|
|
|
120 },
|
|
|
121 "post_job_actions": {},
|
|
|
122 "tool_errors": null,
|
|
|
123 "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/methyation_extractor_tool/0.7.6",
|
|
|
124 "tool_state": "{\"__page__\": 0, \"bamfile\": \"null\", \"ending\": \"\\\"paired\\\"\", \"no_overlap\": \"\\\"ON\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\", \"report\": \"\\\"ON\\\"\"}",
|
|
|
125 "tool_version": "0.7.6",
|
|
|
126 "type": "tool",
|
|
|
127 "user_outputs": []
|
|
|
128 },
|
|
|
129 "4": {
|
|
|
130 "annotation": "",
|
|
|
131 "id": 4,
|
|
|
132 "input_connections": {
|
|
|
133 "bedgraph": {
|
|
|
134 "id": 2,
|
|
|
135 "output_name": "output"
|
|
|
136 }
|
|
|
137 },
|
|
|
138 "inputs": [],
|
|
|
139 "name": "Methylation by Region Converter",
|
|
|
140 "outputs": [
|
|
|
141 {
|
|
|
142 "name": "output",
|
|
|
143 "type": "tabular"
|
|
|
144 },
|
|
|
145 {
|
|
|
146 "name": "summary",
|
|
|
147 "type": "txt"
|
|
|
148 }
|
|
|
149 ],
|
|
|
150 "position": {
|
|
|
151 "left": 673,
|
|
|
152 "top": 221
|
|
|
153 },
|
|
|
154 "post_job_actions": {},
|
|
|
155 "tool_errors": null,
|
|
|
156 "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/methyation_by_region_tool/0.1.1",
|
|
|
157 "tool_state": "{\"sample\": \"\\\"None\\\"\", \"__page__\": 0, \"refBedSource\": \"{\\\"index\\\": \\\"bismark.bed.agilent.human\\\", \\\"__current_case__\\\": 0, \\\"bedSource\\\": \\\"indexed\\\"}\", \"bedgraph\": \"null\"}",
|
|
|
158 "tool_version": "0.1.1",
|
|
|
159 "type": "tool",
|
|
|
160 "user_outputs": []
|
|
|
161 },
|
|
|
162 "5": {
|
|
|
163 "annotation": "",
|
|
|
164 "id": 5,
|
|
|
165 "input_connections": {
|
|
|
166 "bedgraph": {
|
|
|
167 "id": 3,
|
|
|
168 "output_name": "output"
|
|
|
169 }
|
|
|
170 },
|
|
|
171 "inputs": [],
|
|
|
172 "name": "Methylation by Region Converter",
|
|
|
173 "outputs": [
|
|
|
174 {
|
|
|
175 "name": "output",
|
|
|
176 "type": "tabular"
|
|
|
177 },
|
|
|
178 {
|
|
|
179 "name": "summary",
|
|
|
180 "type": "txt"
|
|
|
181 }
|
|
|
182 ],
|
|
|
183 "position": {
|
|
|
184 "left": 674,
|
|
|
185 "top": 397
|
|
|
186 },
|
|
|
187 "post_job_actions": {},
|
|
|
188 "tool_errors": null,
|
|
|
189 "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/methyation_by_region_tool/0.1.1",
|
|
|
190 "tool_state": "{\"sample\": \"\\\"None\\\"\", \"__page__\": 0, \"refBedSource\": \"{\\\"index\\\": \\\"bismark.bed.agilent.human\\\", \\\"__current_case__\\\": 0, \\\"bedSource\\\": \\\"indexed\\\"}\", \"bedgraph\": \"null\"}",
|
|
|
191 "tool_version": "0.1.1",
|
|
|
192 "type": "tool",
|
|
|
193 "user_outputs": []
|
|
|
194 },
|
|
|
195 "6": {
|
|
|
196 "annotation": "",
|
|
|
197 "id": 6,
|
|
|
198 "input_connections": {
|
|
|
199 "seg1": {
|
|
|
200 "id": 4,
|
|
|
201 "output_name": "output"
|
|
|
202 },
|
|
|
203 "seg2": {
|
|
|
204 "id": 5,
|
|
|
205 "output_name": "output"
|
|
|
206 }
|
|
|
207 },
|
|
|
208 "inputs": [],
|
|
|
209 "name": "Differential Methylation",
|
|
|
210 "outputs": [
|
|
|
211 {
|
|
|
212 "name": "output",
|
|
|
213 "type": "tabular"
|
|
|
214 }
|
|
|
215 ],
|
|
|
216 "position": {
|
|
|
217 "left": 993,
|
|
|
218 "top": 308
|
|
|
219 },
|
|
|
220 "post_job_actions": {},
|
|
|
221 "tool_errors": null,
|
|
|
222 "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_bismark/differential_methylation_tool/1.0.0",
|
|
|
223 "tool_state": "{\"__page__\": 0, \"seg1\": \"null\", \"annot\": \"\\\"both\\\"\", \"seg2\": \"null\", \"fdr\": \"\\\"none\\\"\", \"genome\": \"\\\"bismark.dm3.BDGP5.25.62\\\"\"}",
|
|
|
224 "tool_version": "1.0.0",
|
|
|
225 "type": "tool",
|
|
|
226 "user_outputs": []
|
|
|
227 }
|
|
|
228 }
|
|
|
229 } |
