annotate rapsodyn/Galaxy-Workflow-rapsosnp_v1.17-4x.ga @ 5:b0cbb9d21aa9 draft

Uploaded
author mcharles
date Mon, 22 Sep 2014 10:19:53 -0400
parents 9332b9da7491
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
2 "a_galaxy_workflow": "true",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
3 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
4 "format-version": "0.1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
5 "name": "rapsosnp v1.17-4x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
6 "steps": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
7 "0": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
8 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
9 "id": 0,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
10 "input_connections": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
11 "inputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
12 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
13 "description": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
14 "name": "READ1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
15 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
16 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
17 "name": "Input dataset",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
18 "outputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
19 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
20 "left": 200,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
21 "top": 1335.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
22 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
23 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
24 "tool_id": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
25 "tool_state": "{\"name\": \"READ1\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
26 "tool_version": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
27 "type": "data_input",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
28 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
29 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
30 "1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
31 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
32 "id": 1,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
33 "input_connections": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
34 "inputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
35 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
36 "description": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
37 "name": "READ2"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
38 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
39 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
40 "name": "Input dataset",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
41 "outputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
42 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
43 "left": 200,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
44 "top": 1420.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
45 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
46 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
47 "tool_id": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
48 "tool_state": "{\"name\": \"READ2\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
49 "tool_version": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
50 "type": "data_input",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
51 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
52 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
53 "2": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
54 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
55 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
56 "input_connections": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
57 "inputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
58 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
59 "description": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
60 "name": "ASSEMBLY"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
61 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
62 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
63 "name": "Input dataset",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
64 "outputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
65 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
66 "left": 3115,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
67 "top": 1361.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
68 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
69 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
70 "tool_id": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
71 "tool_state": "{\"name\": \"ASSEMBLY\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
72 "tool_version": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
73 "type": "data_input",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
74 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
75 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
76 "3": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
77 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
78 "id": 3,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
79 "input_connections": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
80 "inputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
81 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
82 "description": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
83 "name": "DUBIOUS"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
84 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
85 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
86 "name": "Input dataset",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
87 "outputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
88 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
89 "left": 2679,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
90 "top": 2014.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
91 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
92 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
93 "tool_id": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
94 "tool_state": "{\"name\": \"DUBIOUS\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
95 "tool_version": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
96 "type": "data_input",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
97 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
98 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
99 "4": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
100 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
101 "id": 4,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
102 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
103 "input_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
104 "id": 0,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
105 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
106 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
107 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
108 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
109 "name": "SplitFile4x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
110 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
111 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
112 "name": "output_file1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
113 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
114 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
115 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
116 "name": "output_file2",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
117 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
118 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
119 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
120 "name": "output_file3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
121 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
122 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
123 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
124 "name": "output_file4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
125 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
126 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
127 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
128 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
129 "left": 487,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
130 "top": 1483
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
131 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
132 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
133 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
134 "tool_id": "SplitFile4x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
135 "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
136 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
137 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
138 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
139 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
140 "5": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
141 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
142 "id": 5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
143 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
144 "input_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
145 "id": 1,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
146 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
147 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
148 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
149 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
150 "name": "SplitFile4x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
151 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
152 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
153 "name": "output_file1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
154 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
155 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
156 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
157 "name": "output_file2",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
158 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
159 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
160 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
161 "name": "output_file3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
162 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
163 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
164 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
165 "name": "output_file4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
166 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
167 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
168 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
169 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
170 "left": 486,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
171 "top": 1767
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
172 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
173 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
174 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
175 "tool_id": "SplitFile4x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
176 "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
177 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
178 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
179 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
180 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
181 "6": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
182 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
183 "id": 6,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
184 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
185 "input_fasta": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
186 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
187 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
188 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
189 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
190 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
191 "name": "fastaGroomerForMakeBlastdb",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
192 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
193 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
194 "name": "output_fasta",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
195 "type": "fasta"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
196 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
197 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
198 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
199 "left": 3163,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
200 "top": 1159.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
201 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
202 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
203 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
204 "tool_id": "fastaGroomerForMakeBlastdb",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
205 "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
206 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
207 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
208 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
209 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
210 "7": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
211 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
212 "id": 7,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
213 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
214 "input_read1_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
215 "id": 4,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
216 "output_name": "output_file1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
217 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
218 "input_read2_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
219 "id": 5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
220 "output_name": "output_file1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
221 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
222 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
223 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
224 "name": "PrepareFastqLight",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
225 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
226 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
227 "name": "output_read1_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
228 "type": "fastqsanger"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
229 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
230 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
231 "name": "output_read2_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
232 "type": "fastqsanger"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
233 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
234 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
235 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
236 "left": 791,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
237 "top": 1329.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
238 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
239 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
240 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
241 "tool_id": "PrepareFastqLight",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
242 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
243 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
244 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
245 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
246 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
247 "8": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
248 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
249 "id": 8,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
250 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
251 "input_read1_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
252 "id": 4,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
253 "output_name": "output_file2"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
254 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
255 "input_read2_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
256 "id": 5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
257 "output_name": "output_file2"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
258 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
259 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
260 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
261 "name": "PrepareFastqLight",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
262 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
263 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
264 "name": "output_read1_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
265 "type": "fastqsanger"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
266 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
267 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
268 "name": "output_read2_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
269 "type": "fastqsanger"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
270 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
271 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
272 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
273 "left": 791,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
274 "top": 1531
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
275 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
276 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
277 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
278 "tool_id": "PrepareFastqLight",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
279 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
280 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
281 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
282 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
283 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
284 "9": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
285 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
286 "id": 9,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
287 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
288 "input_read1_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
289 "id": 4,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
290 "output_name": "output_file3"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
291 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
292 "input_read2_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
293 "id": 5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
294 "output_name": "output_file3"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
295 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
296 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
297 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
298 "name": "PrepareFastqLight",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
299 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
300 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
301 "name": "output_read1_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
302 "type": "fastqsanger"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
303 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
304 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
305 "name": "output_read2_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
306 "type": "fastqsanger"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
307 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
308 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
309 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
310 "left": 793,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
311 "top": 1729
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
312 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
313 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
314 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
315 "tool_id": "PrepareFastqLight",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
316 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
317 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
318 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
319 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
320 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
321 "10": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
322 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
323 "id": 10,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
324 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
325 "input_read1_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
326 "id": 4,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
327 "output_name": "output_file4"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
328 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
329 "input_read2_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
330 "id": 5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
331 "output_name": "output_file4"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
332 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
333 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
334 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
335 "name": "PrepareFastqLight",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
336 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
337 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
338 "name": "output_read1_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
339 "type": "fastqsanger"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
340 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
341 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
342 "name": "output_read2_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
343 "type": "fastqsanger"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
344 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
345 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
346 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
347 "left": 795,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
348 "top": 1950
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
349 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
350 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
351 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
352 "tool_id": "PrepareFastqLight",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
353 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
354 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
355 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
356 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
357 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
358 "11": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
359 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
360 "id": 11,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
361 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
362 "input_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
363 "id": 6,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
364 "output_name": "output_fasta"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
365 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
366 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
367 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
368 "name": "NCBI BLAST+ makeblastdb",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
369 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
370 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
371 "name": "outfile",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
372 "type": "data"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
373 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
374 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
375 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
376 "left": 3631,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
377 "top": 1292.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
378 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
379 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
380 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
381 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
382 "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"title\": \"\\\"\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
383 "tool_version": "0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
384 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
385 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
386 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
387 "12": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
388 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
389 "id": 12,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
390 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
391 "genomeSource|ownFile": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
392 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
393 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
394 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
395 "paired|input1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
396 "id": 7,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
397 "output_name": "output_read1_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
398 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
399 "paired|input2": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
400 "id": 7,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
401 "output_name": "output_read2_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
402 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
403 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
404 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
405 "name": "Map with BWA for Illumina",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
406 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
407 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
408 "name": "output",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
409 "type": "sam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
410 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
411 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
412 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
413 "left": 1210,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
414 "top": 1333.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
415 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
416 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
417 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
418 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
419 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
420 "tool_version": "1.2.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
421 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
422 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
423 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
424 "13": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
425 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
426 "id": 13,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
427 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
428 "genomeSource|ownFile": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
429 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
430 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
431 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
432 "paired|input1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
433 "id": 8,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
434 "output_name": "output_read1_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
435 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
436 "paired|input2": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
437 "id": 8,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
438 "output_name": "output_read2_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
439 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
440 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
441 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
442 "name": "Map with BWA for Illumina",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
443 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
444 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
445 "name": "output",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
446 "type": "sam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
447 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
448 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
449 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
450 "left": 1212.5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
451 "top": 1541
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
452 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
453 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
454 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
455 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
456 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
457 "tool_version": "1.2.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
458 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
459 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
460 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
461 "14": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
462 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
463 "id": 14,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
464 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
465 "genomeSource|ownFile": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
466 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
467 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
468 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
469 "paired|input1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
470 "id": 9,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
471 "output_name": "output_read1_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
472 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
473 "paired|input2": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
474 "id": 9,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
475 "output_name": "output_read2_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
476 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
477 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
478 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
479 "name": "Map with BWA for Illumina",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
480 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
481 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
482 "name": "output",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
483 "type": "sam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
484 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
485 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
486 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
487 "left": 1217.5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
488 "top": 1732
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
489 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
490 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
491 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
492 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
493 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
494 "tool_version": "1.2.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
495 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
496 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
497 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
498 "15": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
499 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
500 "id": 15,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
501 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
502 "genomeSource|ownFile": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
503 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
504 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
505 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
506 "paired|input1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
507 "id": 10,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
508 "output_name": "output_read1_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
509 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
510 "paired|input2": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
511 "id": 10,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
512 "output_name": "output_read2_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
513 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
514 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
515 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
516 "name": "Map with BWA for Illumina",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
517 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
518 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
519 "name": "output",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
520 "type": "sam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
521 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
522 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
523 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
524 "left": 1205.5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
525 "top": 1966
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
526 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
527 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
528 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
529 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
530 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
531 "tool_version": "1.2.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
532 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
533 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
534 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
535 "16": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
536 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
537 "id": 16,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
538 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
539 "input_sam_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
540 "id": 12,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
541 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
542 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
543 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
544 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
545 "name": "filtersam_mapped_and_unique",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
546 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
547 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
548 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
549 "type": "sam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
550 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
551 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
552 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
553 "left": 1533,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
554 "top": 1423.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
555 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
556 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
557 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
558 "tool_id": "filtersam_mapped_and_unique",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
559 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
560 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
561 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
562 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
563 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
564 "17": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
565 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
566 "id": 17,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
567 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
568 "input_sam_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
569 "id": 13,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
570 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
571 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
572 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
573 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
574 "name": "filtersam_mapped_and_unique",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
575 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
576 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
577 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
578 "type": "sam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
579 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
580 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
581 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
582 "left": 1528,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
583 "top": 1632
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
584 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
585 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
586 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
587 "tool_id": "filtersam_mapped_and_unique",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
588 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
589 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
590 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
591 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
592 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
593 "18": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
594 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
595 "id": 18,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
596 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
597 "input_sam_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
598 "id": 14,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
599 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
600 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
601 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
602 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
603 "name": "filtersam_mapped_and_unique",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
604 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
605 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
606 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
607 "type": "sam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
608 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
609 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
610 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
611 "left": 1527,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
612 "top": 1805
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
613 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
614 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
615 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
616 "tool_id": "filtersam_mapped_and_unique",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
617 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
618 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
619 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
620 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
621 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
622 "19": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
623 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
624 "id": 19,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
625 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
626 "input_sam_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
627 "id": 15,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
628 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
629 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
630 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
631 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
632 "name": "filtersam_mapped_and_unique",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
633 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
634 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
635 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
636 "type": "sam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
637 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
638 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
639 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
640 "left": 1533,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
641 "top": 2001
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
642 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
643 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
644 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
645 "tool_id": "filtersam_mapped_and_unique",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
646 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
647 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
648 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
649 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
650 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
651 "20": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
652 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
653 "id": 20,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
654 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
655 "source|input1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
656 "id": 16,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
657 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
658 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
659 "source|ref_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
660 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
661 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
662 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
663 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
664 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
665 "name": "SAM-to-BAM",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
666 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
667 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
668 "name": "output1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
669 "type": "bam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
670 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
671 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
672 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
673 "left": 1920,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
674 "top": 1554.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
675 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
676 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
677 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
678 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
679 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
680 "tool_version": "1.1.4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
681 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
682 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
683 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
684 "21": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
685 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
686 "id": 21,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
687 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
688 "source|input1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
689 "id": 17,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
690 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
691 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
692 "source|ref_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
693 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
694 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
695 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
696 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
697 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
698 "name": "SAM-to-BAM",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
699 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
700 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
701 "name": "output1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
702 "type": "bam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
703 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
704 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
705 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
706 "left": 1919,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
707 "top": 1736
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
708 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
709 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
710 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
711 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
712 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
713 "tool_version": "1.1.4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
714 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
715 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
716 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
717 "22": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
718 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
719 "id": 22,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
720 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
721 "source|input1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
722 "id": 18,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
723 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
724 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
725 "source|ref_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
726 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
727 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
728 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
729 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
730 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
731 "name": "SAM-to-BAM",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
732 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
733 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
734 "name": "output1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
735 "type": "bam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
736 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
737 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
738 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
739 "left": 1921,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
740 "top": 1873
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
741 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
742 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
743 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
744 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
745 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
746 "tool_version": "1.1.4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
747 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
748 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
749 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
750 "23": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
751 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
752 "id": 23,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
753 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
754 "source|input1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
755 "id": 19,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
756 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
757 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
758 "source|ref_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
759 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
760 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
761 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
762 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
763 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
764 "name": "SAM-to-BAM",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
765 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
766 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
767 "name": "output1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
768 "type": "bam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
769 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
770 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
771 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
772 "left": 1923,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
773 "top": 2007
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
774 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
775 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
776 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
777 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
778 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
779 "tool_version": "1.1.4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
780 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
781 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
782 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
783 "24": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
784 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
785 "id": 24,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
786 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
787 "input1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
788 "id": 20,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
789 "output_name": "output1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
790 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
791 "input2": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
792 "id": 21,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
793 "output_name": "output1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
794 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
795 "inputs_0|input": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
796 "id": 22,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
797 "output_name": "output1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
798 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
799 "inputs_1|input": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
800 "id": 23,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
801 "output_name": "output1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
802 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
803 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
804 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
805 "name": "Merge BAM Files",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
806 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
807 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
808 "name": "output1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
809 "type": "bam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
810 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
811 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
812 "name": "outlog",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
813 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
814 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
815 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
816 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
817 "left": 2163,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
818 "top": 1680
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
819 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
820 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
821 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
822 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.1.2",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
823 "tool_state": "{\"input2\": \"null\", \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}, {\\\"__index__\\\": 1, \\\"input\\\": null}]\", \"input1\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"title\": \"\\\"None\\\"\", \"mergeSD\": \"\\\"True\\\"\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
824 "tool_version": "1.1.2",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
825 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
826 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
827 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
828 "25": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
829 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
830 "id": 25,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
831 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
832 "reference_source|input_bams_0|input_bam": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
833 "id": 24,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
834 "output_name": "output1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
835 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
836 "reference_source|ref_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
837 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
838 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
839 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
840 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
841 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
842 "name": "MPileup",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
843 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
844 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
845 "name": "output_mpileup",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
846 "type": "pileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
847 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
848 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
849 "name": "output_log",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
850 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
851 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
852 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
853 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
854 "left": 2374,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
855 "top": 1691.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
856 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
857 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
858 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
859 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
860 "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"250\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"30\\\", \\\"disable_probabilistic_realignment\\\": \\\"False\\\", \\\"skip_anomalous_read_pairs\\\": \\\"False\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
861 "tool_version": "0.0.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
862 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
863 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
864 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
865 "26": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
866 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
867 "id": 26,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
868 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
869 "input_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
870 "id": 25,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
871 "output_name": "output_mpileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
872 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
873 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
874 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
875 "name": "PileupVariant",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
876 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
877 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
878 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
879 "type": "pileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
880 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
881 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
882 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
883 "left": 2545,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
884 "top": 1519.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
885 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
886 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
887 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
888 "tool_id": "PileupVariant",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
889 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
890 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
891 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
892 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
893 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
894 "27": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
895 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
896 "id": 27,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
897 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
898 "input_listA": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
899 "id": 26,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
900 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
901 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
902 "input_listB": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
903 "id": 3,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
904 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
905 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
906 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
907 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
908 "name": "listfiltering",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
909 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
910 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
911 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
912 "type": "pileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
913 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
914 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
915 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
916 "left": 2939,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
917 "top": 1599.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
918 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
919 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
920 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
921 "tool_id": "listfiltering",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
922 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_listB\": \"null\", \"nb_col\": \"\\\"2\\\"\", \"input_listA\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
923 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
924 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
925 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
926 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
927 "28": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
928 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
929 "id": 28,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
930 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
931 "input_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
932 "id": 27,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
933 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
934 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
935 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
936 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
937 "name": "SplitFile4x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
938 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
939 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
940 "name": "output_file1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
941 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
942 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
943 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
944 "name": "output_file2",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
945 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
946 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
947 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
948 "name": "output_file3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
949 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
950 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
951 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
952 "name": "output_file4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
953 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
954 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
955 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
956 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
957 "left": 3267,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
958 "top": 1599
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
959 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
960 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
961 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
962 "tool_id": "SplitFile4x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
963 "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
964 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
965 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
966 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
967 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
968 "29": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
969 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
970 "id": 29,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
971 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
972 "input_assembly_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
973 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
974 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
975 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
976 "input_variant_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
977 "id": 28,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
978 "output_name": "output_file1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
979 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
980 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
981 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
982 "name": "extractseq",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
983 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
984 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
985 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
986 "type": "fasta"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
987 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
988 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
989 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
990 "left": 3662,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
991 "top": 1500.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
992 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
993 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
994 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
995 "tool_id": "extractseq",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
996 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
997 "tool_version": "0.03",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
998 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
999 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1000 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1001 "30": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1002 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1003 "id": 30,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1004 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1005 "input_assembly_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1006 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1007 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1008 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1009 "input_variant_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1010 "id": 28,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1011 "output_name": "output_file2"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1012 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1013 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1014 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1015 "name": "extractseq",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1016 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1017 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1018 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1019 "type": "fasta"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1020 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1021 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1022 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1023 "left": 3656,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1024 "top": 1683
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1025 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1026 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1027 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1028 "tool_id": "extractseq",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1029 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1030 "tool_version": "0.03",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1031 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1032 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1033 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1034 "31": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1035 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1036 "id": 31,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1037 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1038 "input_assembly_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1039 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1040 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1041 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1042 "input_variant_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1043 "id": 28,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1044 "output_name": "output_file3"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1045 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1046 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1047 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1048 "name": "extractseq",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1049 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1050 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1051 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1052 "type": "fasta"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1053 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1054 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1055 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1056 "left": 3662,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1057 "top": 1850
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1058 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1059 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1060 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1061 "tool_id": "extractseq",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1062 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1063 "tool_version": "0.03",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1064 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1065 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1066 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1067 "32": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1068 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1069 "id": 32,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1070 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1071 "input_assembly_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1072 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1073 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1074 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1075 "input_variant_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1076 "id": 28,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1077 "output_name": "output_file4"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1078 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1079 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1080 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1081 "name": "extractseq",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1082 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1083 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1084 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1085 "type": "fasta"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1086 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1087 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1088 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1089 "left": 3668,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1090 "top": 2031
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1091 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1092 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1093 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1094 "tool_id": "extractseq",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1095 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1096 "tool_version": "0.03",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1097 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1098 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1099 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1100 "33": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1101 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1102 "id": 33,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1103 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1104 "db_opts|histdb": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1105 "id": 11,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1106 "output_name": "outfile"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1107 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1108 "query": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1109 "id": 29,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1110 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1111 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1112 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1113 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1114 "name": "NCBI BLAST+ blastn",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1115 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1116 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1117 "name": "output1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1118 "type": "tabular"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1119 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1120 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1121 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1122 "left": 4008,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1123 "top": 1477.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1124 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1125 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1126 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1127 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1128 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1129 "tool_version": "0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1130 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1131 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1132 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1133 "34": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1134 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1135 "id": 34,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1136 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1137 "db_opts|histdb": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1138 "id": 11,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1139 "output_name": "outfile"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1140 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1141 "query": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1142 "id": 30,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1143 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1144 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1145 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1146 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1147 "name": "NCBI BLAST+ blastn",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1148 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1149 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1150 "name": "output1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1151 "type": "tabular"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1152 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1153 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1154 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1155 "left": 4011,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1156 "top": 1639
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1157 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1158 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1159 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1160 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1161 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1162 "tool_version": "0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1163 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1164 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1165 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1166 "35": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1167 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1168 "id": 35,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1169 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1170 "db_opts|histdb": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1171 "id": 11,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1172 "output_name": "outfile"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1173 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1174 "query": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1175 "id": 31,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1176 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1177 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1178 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1179 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1180 "name": "NCBI BLAST+ blastn",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1181 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1182 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1183 "name": "output1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1184 "type": "tabular"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1185 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1186 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1187 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1188 "left": 4015,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1189 "top": 1837
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1190 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1191 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1192 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1193 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1194 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1195 "tool_version": "0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1196 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1197 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1198 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1199 "36": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1200 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1201 "id": 36,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1202 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1203 "db_opts|histdb": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1204 "id": 11,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1205 "output_name": "outfile"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1206 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1207 "query": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1208 "id": 32,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1209 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1210 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1211 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1212 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1213 "name": "NCBI BLAST+ blastn",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1214 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1215 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1216 "name": "output1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1217 "type": "tabular"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1218 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1219 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1220 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1221 "left": 4013,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1222 "top": 2038
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1223 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1224 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1225 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1226 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1227 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1228 "tool_version": "0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1229 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1230 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1231 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1232 "37": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1233 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1234 "id": 37,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1235 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1236 "input_blast_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1237 "id": 33,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1238 "output_name": "output1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1239 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1240 "input_variant_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1241 "id": 28,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1242 "output_name": "output_file1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1243 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1244 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1245 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1246 "name": "ParseBlastForUniqueMatch",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1247 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1248 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1249 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1250 "type": "pileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1251 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1252 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1253 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1254 "left": 4304,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1255 "top": 1345.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1256 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1257 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1258 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1259 "tool_id": "ParseBlastForUniqueMatch",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1260 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1261 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1262 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1263 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1264 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1265 "38": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1266 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1267 "id": 38,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1268 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1269 "input_blast_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1270 "id": 34,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1271 "output_name": "output1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1272 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1273 "input_variant_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1274 "id": 28,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1275 "output_name": "output_file2"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1276 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1277 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1278 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1279 "name": "ParseBlastForUniqueMatch",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1280 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1281 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1282 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1283 "type": "pileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1284 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1285 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1286 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1287 "left": 4303.5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1288 "top": 1559
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1289 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1290 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1291 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1292 "tool_id": "ParseBlastForUniqueMatch",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1293 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1294 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1295 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1296 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1297 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1298 "39": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1299 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1300 "id": 39,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1301 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1302 "input_blast_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1303 "id": 35,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1304 "output_name": "output1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1305 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1306 "input_variant_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1307 "id": 28,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1308 "output_name": "output_file3"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1309 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1310 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1311 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1312 "name": "ParseBlastForUniqueMatch",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1313 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1314 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1315 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1316 "type": "pileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1317 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1318 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1319 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1320 "left": 4304.5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1321 "top": 1776
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1322 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1323 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1324 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1325 "tool_id": "ParseBlastForUniqueMatch",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1326 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1327 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1328 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1329 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1330 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1331 "40": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1332 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1333 "id": 40,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1334 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1335 "input_blast_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1336 "id": 36,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1337 "output_name": "output1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1338 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1339 "input_variant_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1340 "id": 28,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1341 "output_name": "output_file4"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1342 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1343 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1344 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1345 "name": "ParseBlastForUniqueMatch",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1346 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1347 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1348 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1349 "type": "pileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1350 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1351 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1352 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1353 "left": 4306.5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1354 "top": 2000
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1355 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1356 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1357 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1358 "tool_id": "ParseBlastForUniqueMatch",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1359 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1360 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1361 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1362 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1363 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1364 "41": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1365 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1366 "id": 41,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1367 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1368 "input_file1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1369 "id": 37,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1370 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1371 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1372 "input_file2": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1373 "id": 38,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1374 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1375 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1376 "input_file3": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1377 "id": 39,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1378 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1379 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1380 "input_file4": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1381 "id": 40,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1382 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1383 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1384 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1385 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1386 "name": "MergeFile4x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1387 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1388 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1389 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1390 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1391 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1392 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1393 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1394 "left": 4718,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1395 "top": 1529
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1396 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1397 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1398 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1399 "tool_id": "MergeFile4x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1400 "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file4\": \"null\", \"input_file1\": \"null\", \"input_file2\": \"null\", \"input_file3\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1401 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1402 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1403 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1404 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1405 "42": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1406 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1407 "id": 42,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1408 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1409 "input_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1410 "id": 41,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1411 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1412 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1413 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1414 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1415 "name": "mpileupfilterandstat",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1416 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1417 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1418 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1419 "type": "pileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1420 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1421 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1422 "name": "log_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1423 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1424 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1425 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1426 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1427 "left": 5089,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1428 "top": 1571
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1429 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1430 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1431 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1432 "tool_id": "mpileupfilterandstat",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1433 "tool_state": "{\"__page__\": 0, \"stat\": \"{\\\"stat_dist_step\\\": \\\"50\\\", \\\"stat_min_depth_step\\\": \\\"2\\\", \\\"stat_max_depth_max\\\": \\\"200\\\", \\\"stat_min_depth_max\\\": \\\"10\\\", \\\"stat_freq_max\\\": \\\"1.0\\\", \\\"stat_min_depth_min\\\": \\\"2\\\", \\\"stat_max_depth_min\\\": \\\"100\\\", \\\"do_stat\\\": \\\"YES\\\", \\\"stat_dist_min\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"stat_max_depth_step\\\": \\\"100\\\", \\\"stat_dist_max\\\": \\\"50\\\", \\\"stat_freq_step\\\": \\\"0.1\\\", \\\"stat_freq_min\\\": \\\"0.8\\\"}\", \"input_file\": \"null\", \"min_frequency\": \"\\\"0.8\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"100\\\"\", \"min_distance\": \"\\\"0\\\"\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1434 "tool_version": "0.08",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1435 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1436 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1437 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1438 "43": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1439 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1440 "id": 43,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1441 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1442 "input_blast_filtered_part1_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1443 "id": 37,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1444 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1445 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1446 "input_blast_filtered_part2_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1447 "id": 38,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1448 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1449 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1450 "input_blast_filtered_part3_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1451 "id": 39,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1452 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1453 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1454 "input_blast_filtered_part4_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1455 "id": 40,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1456 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1457 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1458 "input_list_filtered_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1459 "id": 27,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1460 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1461 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1462 "input_mpileup_variant_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1463 "id": 26,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1464 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1465 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1466 "input_read1_part1_trimmed_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1467 "id": 7,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1468 "output_name": "output_read1_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1469 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1470 "input_read1_part2_trimmed_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1471 "id": 8,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1472 "output_name": "output_read1_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1473 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1474 "input_read1_part3_trimmed_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1475 "id": 9,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1476 "output_name": "output_read1_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1477 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1478 "input_read1_part4_trimmed_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1479 "id": 10,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1480 "output_name": "output_read1_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1481 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1482 "input_read1_row_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1483 "id": 0,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1484 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1485 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1486 "input_read2_part1_trimmed_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1487 "id": 7,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1488 "output_name": "output_read2_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1489 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1490 "input_read2_part2_trimmed_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1491 "id": 8,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1492 "output_name": "output_read2_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1493 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1494 "input_read2_part3_trimmed_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1495 "id": 9,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1496 "output_name": "output_read2_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1497 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1498 "input_read2_part4_trimmed_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1499 "id": 10,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1500 "output_name": "output_read2_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1501 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1502 "input_read2_row_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1503 "id": 1,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1504 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1505 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1506 "input_sam_filtered_part1_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1507 "id": 16,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1508 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1509 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1510 "input_sam_filtered_part2_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1511 "id": 17,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1512 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1513 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1514 "input_sam_filtered_part3_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1515 "id": 18,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1516 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1517 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1518 "input_sam_filtered_part4_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1519 "id": 19,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1520 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1521 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1522 "input_sam_row_part1_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1523 "id": 12,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1524 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1525 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1526 "input_sam_row_part2_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1527 "id": 13,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1528 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1529 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1530 "input_sam_row_part3_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1531 "id": 14,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1532 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1533 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1534 "input_sam_row_part4_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1535 "id": 15,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1536 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1537 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1538 "input_snp_selected_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1539 "id": 42,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1540 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1541 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1542 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1543 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1544 "name": "rapsosnp_stats4x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1545 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1546 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1547 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1548 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1549 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1550 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1551 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1552 "left": 1883.5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1553 "top": 200
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1554 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1555 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1556 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1557 "tool_id": "rapsosnp_stats4x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1558 "tool_state": "{\"input_blast_filtered_part2_file\": \"null\", \"input_blast_filtered_part3_file\": \"null\", \"input_read2_part1_trimmed_file\": \"null\", \"input_read1_row_file\": \"null\", \"input_read1_part2_trimmed_file\": \"null\", \"input_read1_part4_trimmed_file\": \"null\", \"input_read1_part3_trimmed_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_mpileup_variant_file\": \"null\", \"input_sam_row_part1_file\": \"null\", \"input_blast_filtered_part1_file\": \"null\", \"input_sam_row_part4_file\": \"null\", \"input_sam_filtered_part1_file\": \"null\", \"input_read2_part3_trimmed_file\": \"null\", \"input_read2_part4_trimmed_file\": \"null\", \"input_sam_filtered_part3_file\": \"null\", \"input_sam_filtered_part4_file\": \"null\", \"input_sam_row_part2_file\": \"null\", \"input_read1_part1_trimmed_file\": \"null\", \"input_read2_row_file\": \"null\", \"input_blast_filtered_part4_file\": \"null\", \"input_sam_row_part3_file\": \"null\", \"input_sam_filtered_part2_file\": \"null\", \"input_read2_part2_trimmed_file\": \"null\", \"input_snp_selected_file\": \"null\", \"input_list_filtered_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1559 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1560 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1561 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1562 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1563 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1564 }