annotate Galaxy-Workflow-MGS-Fast_pipeline.ga @ 0:8f9b6edb6240 draft default tip

Uploaded
author ntino
date Sat, 05 May 2018 12:47:57 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
1 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
2 "a_galaxy_workflow": "true",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
3 "annotation": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
4 "format-version": "0.1",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
5 "name": "Parallel MGS-Fast pipeline'",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
6 "steps": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
7 "0": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
8 "annotation": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
9 "id": 0,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
10 "input_connections": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
11 "inputs": [
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
12 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
13 "description": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
14 "name": "MGS Paired-End Reads 1"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
15 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
16 ],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
17 "label": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
18 "name": "Input dataset",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
19 "outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
20 "position": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
21 "left": 207.03125,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
22 "top": 440.984375
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
23 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
24 "tool_errors": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
25 "tool_id": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
26 "tool_state": "{\"name\": \"MGS Paired-End Reads 1\"}",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
27 "tool_version": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
28 "type": "data_input",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
29 "user_outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
30 "uuid": "590833d5-cf50-4080-aca8-09bf60edf9cb"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
31 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
32 "1": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
33 "annotation": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
34 "id": 1,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
35 "input_connections": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
36 "inputs": [
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
37 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
38 "description": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
39 "name": "MGS Paired-End Reads 2"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
40 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
41 ],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
42 "label": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
43 "name": "Input dataset",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
44 "outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
45 "position": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
46 "left": 200,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
47 "top": 523.96875
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
48 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
49 "tool_errors": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
50 "tool_id": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
51 "tool_state": "{\"name\": \"MGS Paired-End Reads 2\"}",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
52 "tool_version": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
53 "type": "data_input",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
54 "user_outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
55 "uuid": "c98deb39-dcfc-49ff-a087-d279e3a6f6ea"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
56 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
57 "2": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
58 "annotation": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
59 "id": 2,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
60 "input_connections": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
61 "input_file": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
62 "id": 0,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
63 "output_name": "output"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
64 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
65 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
66 "inputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
67 "label": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
68 "name": "FastQC",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
69 "outputs": [
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
70 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
71 "name": "html_file",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
72 "type": "html"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
73 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
74 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
75 "name": "text_file",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
76 "type": "txt"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
77 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
78 ],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
79 "position": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
80 "left": 394.015625,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
81 "top": 203
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
82 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
83 "post_job_actions": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
84 "HideDatasetActiontext_file": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
85 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
86 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
87 "output_name": "text_file"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
88 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
89 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
90 "tool_errors": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
91 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.63",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
92 "tool_state": "{\"__page__\": 0, \"contaminants\": \"null\", \"__rerun_remap_job_id__\": null, \"limits\": \"null\", \"input_file\": \"null\"}",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
93 "tool_version": "0.63",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
94 "type": "tool",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
95 "user_outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
96 "uuid": "ece63296-d0de-4fa6-9eb0-a3539cc8d2ea"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
97 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
98 "3": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
99 "annotation": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
100 "id": 3,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
101 "input_connections": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
102 "input_file": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
103 "id": 0,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
104 "output_name": "output"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
105 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
106 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
107 "inputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
108 "label": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
109 "name": "FASTQ Groomer",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
110 "outputs": [
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
111 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
112 "name": "output_file",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
113 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
114 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
115 ],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
116 "position": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
117 "left": 499.484375,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
118 "top": 474.890625
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
119 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
120 "post_job_actions": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
121 "tool_errors": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
122 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
123 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
124 "tool_version": "1.0.4",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
125 "type": "tool",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
126 "user_outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
127 "uuid": "1bedb876-1e75-4e66-a387-8ff098ba6af4"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
128 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
129 "4": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
130 "annotation": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
131 "id": 4,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
132 "input_connections": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
133 "input_file": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
134 "id": 1,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
135 "output_name": "output"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
136 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
137 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
138 "inputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
139 "label": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
140 "name": "FastQC",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
141 "outputs": [
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
142 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
143 "name": "html_file",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
144 "type": "html"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
145 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
146 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
147 "name": "text_file",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
148 "type": "txt"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
149 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
150 ],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
151 "position": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
152 "left": 726.109375,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
153 "top": 206.09375
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
154 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
155 "post_job_actions": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
156 "HideDatasetActiontext_file": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
157 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
158 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
159 "output_name": "text_file"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
160 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
161 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
162 "tool_errors": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
163 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.63",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
164 "tool_state": "{\"__page__\": 0, \"contaminants\": \"null\", \"__rerun_remap_job_id__\": null, \"limits\": \"null\", \"input_file\": \"null\"}",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
165 "tool_version": "0.63",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
166 "type": "tool",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
167 "user_outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
168 "uuid": "121b4c76-2f3f-4b42-9e2a-629735613e07"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
169 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
170 "5": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
171 "annotation": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
172 "id": 5,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
173 "input_connections": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
174 "input_file": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
175 "id": 1,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
176 "output_name": "output"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
177 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
178 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
179 "inputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
180 "label": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
181 "name": "FASTQ Groomer",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
182 "outputs": [
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
183 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
184 "name": "output_file",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
185 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
186 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
187 ],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
188 "position": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
189 "left": 481.65625,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
190 "top": 657.03125
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
191 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
192 "post_job_actions": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
193 "HideDatasetActionoutput_file": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
194 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
195 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
196 "output_name": "output_file"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
197 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
198 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
199 "tool_errors": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
200 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
201 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
202 "tool_version": "1.0.4",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
203 "type": "tool",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
204 "user_outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
205 "uuid": "0bb1887b-bdc4-4709-be81-18e1340317e9"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
206 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
207 "6": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
208 "annotation": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
209 "id": 6,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
210 "input_connections": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
211 "paired_end|fastq_r1_in": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
212 "id": 3,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
213 "output_name": "output_file"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
214 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
215 "paired_end|fastq_r2_in": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
216 "id": 5,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
217 "output_name": "output_file"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
218 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
219 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
220 "inputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
221 "label": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
222 "name": "Trimmomatic",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
223 "outputs": [
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
224 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
225 "name": "fastq_out_r1_paired",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
226 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
227 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
228 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
229 "name": "fastq_out_r1_unpaired",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
230 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
231 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
232 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
233 "name": "fastq_out_r2_paired",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
234 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
235 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
236 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
237 "name": "fastq_out_r2_unpaired",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
238 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
239 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
240 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
241 "name": "fastq_out",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
242 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
243 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
244 ],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
245 "position": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
246 "left": 806.453125,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
247 "top": 559.859375
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
248 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
249 "post_job_actions": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
250 "HideDatasetActionfastq_out": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
251 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
252 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
253 "output_name": "fastq_out"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
254 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
255 "HideDatasetActionfastq_out_r1_unpaired": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
256 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
257 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
258 "output_name": "fastq_out_r1_unpaired"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
259 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
260 "HideDatasetActionfastq_out_r2_unpaired": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
261 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
262 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
263 "output_name": "fastq_out_r2_unpaired"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
264 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
265 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
266 "tool_errors": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
267 "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.1",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
268 "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"window_size\\\": \\\"4\\\", \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"__current_case__\\\": 0, \\\"required_quality\\\": \\\"20\\\"}}]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_end\": \"{\\\"is_paired_end\\\": \\\"True\\\", \\\"fastq_r1_in\\\": null, \\\"__current_case__\\\": 1, \\\"fastq_r2_in\\\": null}\", \"illuminaclip\": \"{\\\"do_illuminaclip\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\"}",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
269 "tool_version": "0.32.1",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
270 "type": "tool",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
271 "user_outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
272 "uuid": "ce378908-0a0d-4728-bb97-a938ccc5fb4a"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
273 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
274 "7": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
275 "annotation": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
276 "id": 7,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
277 "input_connections": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
278 "library|input_1": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
279 "id": 6,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
280 "output_name": "fastq_out_r1_paired"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
281 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
282 "library|input_2": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
283 "id": 6,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
284 "output_name": "fastq_out_r2_paired"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
285 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
286 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
287 "inputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
288 "label": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
289 "name": "Bowtie2",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
290 "outputs": [
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
291 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
292 "name": "output_unaligned_reads_l",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
293 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
294 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
295 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
296 "name": "output_aligned_reads_l",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
297 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
298 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
299 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
300 "name": "output_aligned_reads_r",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
301 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
302 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
303 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
304 "name": "output_unaligned_reads_r",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
305 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
306 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
307 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
308 "name": "output",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
309 "type": "bam"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
310 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
311 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
312 "name": "output_sam",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
313 "type": "sam"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
314 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
315 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
316 "name": "mapping_stats",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
317 "type": "txt"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
318 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
319 ],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
320 "position": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
321 "left": 1173,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
322 "top": 575.5
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
323 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
324 "post_job_actions": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
325 "HideDatasetActionmapping_stats": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
326 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
327 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
328 "output_name": "mapping_stats"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
329 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
330 "HideDatasetActionoutput": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
331 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
332 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
333 "output_name": "output"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
334 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
335 "HideDatasetActionoutput_aligned_reads_l": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
336 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
337 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
338 "output_name": "output_aligned_reads_l"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
339 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
340 "HideDatasetActionoutput_aligned_reads_r": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
341 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
342 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
343 "output_name": "output_aligned_reads_r"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
344 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
345 "HideDatasetActionoutput_sam": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
346 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
347 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
348 "output_name": "output_sam"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
349 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
350 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
351 "tool_errors": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
352 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
353 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"False\\\", \\\"unaligned_file\\\": \\\"True\\\", \\\"input_2\\\": null, \\\"__current_case__\\\": 1, \\\"input_1\\\": null, \\\"type\\\": \\\"paired\\\", \\\"paired_options\\\": {\\\"no_mixed\\\": \\\"False\\\", \\\"dovetail\\\": \\\"False\\\", \\\"I\\\": \\\"0\\\", \\\"no_contain\\\": \\\"False\\\", \\\"no_discordant\\\": \\\"True\\\", \\\"no_overlap\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"X\\\": \\\"1000\\\", \\\"fr_rf_ff\\\": \\\"--fr\\\", \\\"paired_options_selector\\\": \\\"yes\\\"}}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"hg38\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"False\\\"\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"simple\\\", \\\"presets\\\": \\\"no_presets\\\", \\\"__current_case__\\\": 0}\"}",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
354 "tool_version": "2.2.6.2",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
355 "type": "tool",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
356 "user_outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
357 "uuid": "075dddd1-df9c-42dd-8025-871a7f619a7f"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
358 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
359 "8": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
360 "annotation": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
361 "id": 8,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
362 "input_connections": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
363 "input": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
364 "id": 7,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
365 "output_name": "output_unaligned_reads_l"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
366 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
367 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
368 "inputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
369 "label": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
370 "name": "MetaPhlAn2",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
371 "outputs": [
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
372 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
373 "name": "output",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
374 "type": "tabular"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
375 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
376 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
377 "name": "biom_output",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
378 "type": "text"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
379 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
380 ],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
381 "position": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
382 "left": 1610.5,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
383 "top": 345
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
384 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
385 "post_job_actions": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
386 "tool_errors": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
387 "tool_id": "toolshed.g2.bx.psu.edu/repos/george-weingart/metaphlan2_hutlab/metaphlan2_hutlab/2.5.0",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
388 "tool_state": "{\"__page__\": 0, \"PresetsForBowtie2\": \"\\\"very-sensitive\\\"\", \"gchoice_biom\": \"{\\\"global_biom\\\": \\\"0\\\", \\\"__current_case__\\\": 0}\", \"gchoice_additional_analysis_types\": \"{\\\"Analysis_Type\\\": \\\"\\\", \\\"global_additional_analysis_types\\\": \\\"0\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"gchoice_post_mapping\": \"{\\\"min_cu_len\\\": \\\"\\\", \\\"__current_case__\\\": 0, \\\"global_choice_post_mapping\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null}",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
389 "tool_version": "2.5.0",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
390 "type": "tool",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
391 "user_outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
392 "uuid": "1289ad82-4813-4282-9955-50473b400f33"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
393 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
394 "9": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
395 "annotation": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
396 "id": 9,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
397 "input_connections": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
398 "input": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
399 "id": 7,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
400 "output_name": "output_unaligned_reads_r"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
401 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
402 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
403 "inputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
404 "label": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
405 "name": "MetaPhlAn2",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
406 "outputs": [
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
407 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
408 "name": "output",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
409 "type": "tabular"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
410 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
411 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
412 "name": "biom_output",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
413 "type": "text"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
414 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
415 ],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
416 "position": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
417 "left": 1613.5,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
418 "top": 515
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
419 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
420 "post_job_actions": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
421 "tool_errors": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
422 "tool_id": "toolshed.g2.bx.psu.edu/repos/george-weingart/metaphlan2_hutlab/metaphlan2_hutlab/2.5.0",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
423 "tool_state": "{\"__page__\": 0, \"PresetsForBowtie2\": \"\\\"very-sensitive\\\"\", \"gchoice_biom\": \"{\\\"global_biom\\\": \\\"0\\\", \\\"__current_case__\\\": 0}\", \"gchoice_additional_analysis_types\": \"{\\\"Analysis_Type\\\": \\\"\\\", \\\"global_additional_analysis_types\\\": \\\"0\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"gchoice_post_mapping\": \"{\\\"min_cu_len\\\": \\\"\\\", \\\"__current_case__\\\": 0, \\\"global_choice_post_mapping\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null}",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
424 "tool_version": "2.5.0",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
425 "type": "tool",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
426 "user_outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
427 "uuid": "166e172a-2c00-49ab-9cc1-6ca1f490ff1f"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
428 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
429 "10": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
430 "annotation": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
431 "id": 10,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
432 "input_connections": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
433 "library|input_1": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
434 "id": 7,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
435 "output_name": "output_unaligned_reads_l"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
436 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
437 "library|input_2": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
438 "id": 7,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
439 "output_name": "output_unaligned_reads_r"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
440 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
441 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
442 "inputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
443 "label": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
444 "name": "Bowtie2",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
445 "outputs": [
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
446 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
447 "name": "output_unaligned_reads_l",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
448 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
449 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
450 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
451 "name": "output_aligned_reads_l",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
452 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
453 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
454 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
455 "name": "output_aligned_reads_r",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
456 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
457 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
458 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
459 "name": "output_unaligned_reads_r",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
460 "type": "fastqsanger"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
461 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
462 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
463 "name": "output",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
464 "type": "bam"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
465 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
466 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
467 "name": "output_sam",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
468 "type": "sam"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
469 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
470 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
471 "name": "mapping_stats",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
472 "type": "txt"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
473 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
474 ],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
475 "position": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
476 "left": 1628,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
477 "top": 715.5
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
478 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
479 "post_job_actions": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
480 "ChangeDatatypeActionoutput": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
481 "action_arguments": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
482 "newtype": "sam"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
483 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
484 "action_type": "ChangeDatatypeAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
485 "output_name": "output"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
486 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
487 "HideDatasetActionmapping_stats": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
488 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
489 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
490 "output_name": "mapping_stats"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
491 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
492 "HideDatasetActionoutput_aligned_reads_l": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
493 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
494 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
495 "output_name": "output_aligned_reads_l"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
496 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
497 "HideDatasetActionoutput_aligned_reads_r": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
498 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
499 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
500 "output_name": "output_aligned_reads_r"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
501 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
502 "HideDatasetActionoutput_unaligned_reads_l": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
503 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
504 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
505 "output_name": "output_unaligned_reads_l"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
506 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
507 "HideDatasetActionoutput_unaligned_reads_r": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
508 "action_arguments": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
509 "action_type": "HideDatasetAction",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
510 "output_name": "output_unaligned_reads_r"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
511 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
512 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
513 "tool_errors": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
514 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
515 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"False\\\", \\\"unaligned_file\\\": \\\"False\\\", \\\"input_2\\\": null, \\\"__current_case__\\\": 1, \\\"input_1\\\": null, \\\"type\\\": \\\"paired\\\", \\\"paired_options\\\": {\\\"paired_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"IGC\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"False\\\"\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"simple\\\", \\\"presets\\\": \\\"--very-sensitive-local\\\", \\\"__current_case__\\\": 0}\"}",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
516 "tool_version": "2.2.6.2",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
517 "type": "tool",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
518 "user_outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
519 "uuid": "80b3aa7d-c494-4a6d-9ec0-028641fc477e"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
520 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
521 "11": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
522 "annotation": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
523 "id": 11,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
524 "input_connections": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
525 "input_file": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
526 "id": 10,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
527 "output_name": "output"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
528 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
529 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
530 "inputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
531 "label": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
532 "name": "Create GeneList Outputs",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
533 "outputs": [
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
534 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
535 "name": "gene",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
536 "type": "txt"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
537 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
538 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
539 "name": "kegg",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
540 "type": "kegg"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
541 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
542 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
543 "name": "list",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
544 "type": "list"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
545 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
546 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
547 "name": "anno_txt",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
548 "type": "txt"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
549 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
550 ],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
551 "position": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
552 "left": 2040.953125,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
553 "top": 651.765625
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
554 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
555 "post_job_actions": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
556 "tool_errors": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
557 "tool_id": "geneList",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
558 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
559 "tool_version": "0.63",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
560 "type": "tool",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
561 "user_outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
562 "uuid": "a6796f6d-0028-45db-9f68-057601c48156"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
563 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
564 "12": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
565 "annotation": "",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
566 "id": 12,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
567 "input_connections": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
568 "input_file": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
569 "id": 11,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
570 "output_name": "gene"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
571 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
572 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
573 "inputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
574 "label": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
575 "name": "Count Keggs",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
576 "outputs": [
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
577 {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
578 "name": "kegg_count",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
579 "type": "txt"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
580 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
581 ],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
582 "position": {
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
583 "left": 2395.953125,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
584 "top": 555.765625
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
585 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
586 "post_job_actions": {},
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
587 "tool_errors": null,
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
588 "tool_id": "countKeggs",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
589 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
590 "tool_version": "0.63",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
591 "type": "tool",
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
592 "user_outputs": [],
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
593 "uuid": "dceeae01-8956-479e-927c-4972a907bc9f"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
594 }
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
595 },
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
596 "uuid": "5378670e-9e06-4b0c-93df-f6cbd41f646a"
8f9b6edb6240 Uploaded
ntino
parents:
diff changeset
597 }