annotate rapsodyn/Galaxy-Workflow-rapsosnp_v1.17-2x.ga @ 4:9074a5104cdd draft

Uploaded
author mcharles
date Wed, 17 Sep 2014 04:20:08 -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 v1.17-2x",
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": 814
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": 899
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": 2916,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
67 "top": 906
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": 1493
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": "SplitFile2x",
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 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
121 "left": 475,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
122 "top": 1049.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
123 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
124 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
125 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
126 "tool_id": "SplitFile2x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
127 "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
128 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
129 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
130 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
131 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
132 "5": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
133 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
134 "id": 5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
135 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
136 "input_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
137 "id": 1,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
138 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
139 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
140 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
141 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
142 "name": "SplitFile2x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
143 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
144 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
145 "name": "output_file1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
146 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
147 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
148 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
149 "name": "output_file2",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
150 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
151 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
152 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
153 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
154 "left": 476,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
155 "top": 1240.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
156 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
157 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
158 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
159 "tool_id": "SplitFile2x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
160 "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
161 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
162 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
163 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
164 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
165 "6": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
166 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
167 "id": 6,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
168 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
169 "input_fasta": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
170 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
171 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
172 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
173 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
174 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
175 "name": "fastaGroomerForMakeBlastdb",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
176 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
177 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
178 "name": "output_fasta",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
179 "type": "fasta"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
180 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
181 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
182 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
183 "left": 3163,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
184 "top": 638
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
185 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
186 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
187 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
188 "tool_id": "fastaGroomerForMakeBlastdb",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
189 "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
190 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
191 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
192 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
193 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
194 "7": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
195 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
196 "id": 7,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
197 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
198 "input_read1_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
199 "id": 4,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
200 "output_name": "output_file1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
201 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
202 "input_read2_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
203 "id": 5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
204 "output_name": "output_file1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
205 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
206 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
207 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
208 "name": "PrepareFastqLight",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
209 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
210 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
211 "name": "output_read1_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
212 "type": "fastqsanger"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
213 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
214 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
215 "name": "output_read2_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
216 "type": "fastqsanger"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
217 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
218 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
219 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
220 "left": 791,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
221 "top": 1053
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
222 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
223 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
224 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
225 "tool_id": "PrepareFastqLight",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
226 "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
227 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
228 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
229 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
230 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
231 "8": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
232 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
233 "id": 8,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
234 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
235 "input_read1_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
236 "id": 4,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
237 "output_name": "output_file2"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
238 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
239 "input_read2_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
240 "id": 5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
241 "output_name": "output_file2"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
242 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
243 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
244 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
245 "name": "PrepareFastqLight",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
246 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
247 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
248 "name": "output_read1_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
249 "type": "fastqsanger"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
250 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
251 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
252 "name": "output_read2_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
253 "type": "fastqsanger"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
254 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
255 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
256 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
257 "left": 792,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
258 "top": 1244.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
259 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
260 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
261 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
262 "tool_id": "PrepareFastqLight",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
263 "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
264 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
265 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
266 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
267 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
268 "9": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
269 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
270 "id": 9,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
271 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
272 "input_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
273 "id": 6,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
274 "output_name": "output_fasta"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
275 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
276 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
277 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
278 "name": "NCBI BLAST+ makeblastdb",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
279 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
280 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
281 "name": "outfile",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
282 "type": "data"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
283 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
284 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
285 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
286 "left": 3561,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
287 "top": 595
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
288 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
289 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
290 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
291 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
292 "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
293 "tool_version": "0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
294 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
295 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
296 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
297 "10": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
298 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
299 "id": 10,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
300 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
301 "genomeSource|ownFile": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
302 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
303 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
304 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
305 "paired|input1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
306 "id": 7,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
307 "output_name": "output_read1_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
308 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
309 "paired|input2": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
310 "id": 7,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
311 "output_name": "output_read2_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
312 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
313 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
314 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
315 "name": "Map with BWA for Illumina",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
316 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
317 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
318 "name": "output",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
319 "type": "sam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
320 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
321 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
322 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
323 "left": 1197,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
324 "top": 998
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
325 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
326 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
327 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
328 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
329 "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
330 "tool_version": "1.2.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
331 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
332 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
333 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
334 "11": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
335 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
336 "id": 11,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
337 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
338 "genomeSource|ownFile": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
339 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
340 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
341 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
342 "paired|input1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
343 "id": 8,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
344 "output_name": "output_read1_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
345 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
346 "paired|input2": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
347 "id": 8,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
348 "output_name": "output_read2_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
349 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
350 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
351 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
352 "name": "Map with BWA for Illumina",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
353 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
354 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
355 "name": "output",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
356 "type": "sam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
357 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
358 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
359 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
360 "left": 1197.5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
361 "top": 1226.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
362 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
363 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
364 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
365 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
366 "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
367 "tool_version": "1.2.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
368 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
369 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
370 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
371 "12": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
372 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
373 "id": 12,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
374 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
375 "input_sam_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
376 "id": 10,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
377 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
378 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
379 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
380 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
381 "name": "filtersam_mapped_and_unique",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
382 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
383 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
384 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
385 "type": "sam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
386 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
387 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
388 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
389 "left": 1571,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
390 "top": 1033
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
391 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
392 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
393 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
394 "tool_id": "filtersam_mapped_and_unique",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
395 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
396 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
397 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
398 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
399 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
400 "13": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
401 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
402 "id": 13,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
403 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
404 "input_sam_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
405 "id": 11,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
406 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
407 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
408 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
409 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
410 "name": "filtersam_mapped_and_unique",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
411 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
412 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
413 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
414 "type": "sam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
415 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
416 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
417 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
418 "left": 1549,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
419 "top": 1215.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
420 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
421 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
422 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
423 "tool_id": "filtersam_mapped_and_unique",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
424 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
425 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
426 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
427 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
428 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
429 "14": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
430 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
431 "id": 14,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
432 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
433 "source|input1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
434 "id": 12,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
435 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
436 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
437 "source|ref_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
438 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
439 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
440 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
441 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
442 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
443 "name": "SAM-to-BAM",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
444 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
445 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
446 "name": "output1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
447 "type": "bam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
448 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
449 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
450 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
451 "left": 1920,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
452 "top": 1033
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
453 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
454 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
455 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
456 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
457 "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
458 "tool_version": "1.1.4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
459 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
460 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
461 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
462 "15": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
463 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
464 "id": 15,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
465 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
466 "source|input1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
467 "id": 13,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
468 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
469 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
470 "source|ref_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
471 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
472 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
473 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
474 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
475 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
476 "name": "SAM-to-BAM",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
477 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
478 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
479 "name": "output1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
480 "type": "bam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
481 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
482 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
483 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
484 "left": 1919,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
485 "top": 1214.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
486 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
487 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
488 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
489 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
490 "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
491 "tool_version": "1.1.4",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
492 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
493 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
494 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
495 "16": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
496 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
497 "id": 16,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
498 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
499 "input1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
500 "id": 14,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
501 "output_name": "output1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
502 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
503 "input2": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
504 "id": 15,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
505 "output_name": "output1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
506 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
507 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
508 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
509 "name": "Merge BAM Files",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
510 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
511 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
512 "name": "output1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
513 "type": "bam"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
514 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
515 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
516 "name": "outlog",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
517 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
518 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
519 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
520 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
521 "left": 2163,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
522 "top": 1158.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
523 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
524 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
525 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
526 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.1.2",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
527 "tool_state": "{\"input2\": \"null\", \"inputs\": \"[]\", \"input1\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"title\": \"\\\"None\\\"\", \"mergeSD\": \"\\\"True\\\"\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
528 "tool_version": "1.1.2",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
529 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
530 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
531 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
532 "17": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
533 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
534 "id": 17,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
535 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
536 "reference_source|input_bams_0|input_bam": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
537 "id": 16,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
538 "output_name": "output1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
539 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
540 "reference_source|ref_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
541 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
542 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
543 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
544 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
545 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
546 "name": "MPileup",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
547 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
548 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
549 "name": "output_mpileup",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
550 "type": "pileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
551 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
552 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
553 "name": "output_log",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
554 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
555 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
556 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
557 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
558 "left": 2374,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
559 "top": 1170
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
560 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
561 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
562 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
563 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
564 "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
565 "tool_version": "0.0.3",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
566 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
567 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
568 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
569 "18": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
570 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
571 "id": 18,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
572 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
573 "input_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
574 "id": 17,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
575 "output_name": "output_mpileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
576 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
577 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
578 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
579 "name": "PileupVariant",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
580 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
581 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
582 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
583 "type": "pileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
584 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
585 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
586 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
587 "left": 2545,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
588 "top": 998
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
589 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
590 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
591 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
592 "tool_id": "PileupVariant",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
593 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
594 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
595 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
596 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
597 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
598 "19": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
599 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
600 "id": 19,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
601 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
602 "input_listA": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
603 "id": 18,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
604 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
605 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
606 "input_listB": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
607 "id": 3,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
608 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
609 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
610 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
611 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
612 "name": "listfiltering",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
613 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
614 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
615 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
616 "type": "pileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
617 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
618 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
619 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
620 "left": 2939,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
621 "top": 1078
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
622 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
623 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
624 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
625 "tool_id": "listfiltering",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
626 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_listB\": \"null\", \"nb_col\": \"\\\"2\\\"\", \"input_listA\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
627 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
628 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
629 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
630 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
631 "20": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
632 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
633 "id": 20,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
634 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
635 "input_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
636 "id": 19,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
637 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
638 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
639 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
640 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
641 "name": "SplitFile2x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
642 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
643 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
644 "name": "output_file1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
645 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
646 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
647 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
648 "name": "output_file2",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
649 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
650 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
651 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
652 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
653 "left": 3292,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
654 "top": 1066.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
655 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
656 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
657 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
658 "tool_id": "SplitFile2x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
659 "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
660 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
661 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
662 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
663 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
664 "21": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
665 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
666 "id": 21,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
667 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
668 "input_assembly_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
669 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
670 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
671 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
672 "input_variant_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
673 "id": 20,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
674 "output_name": "output_file1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
675 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
676 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
677 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
678 "name": "extractseq",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
679 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
680 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
681 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
682 "type": "fasta"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
683 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
684 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
685 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
686 "left": 3662,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
687 "top": 979
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
688 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
689 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
690 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
691 "tool_id": "extractseq",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
692 "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
693 "tool_version": "0.03",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
694 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
695 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
696 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
697 "22": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
698 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
699 "id": 22,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
700 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
701 "input_assembly_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
702 "id": 2,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
703 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
704 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
705 "input_variant_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
706 "id": 20,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
707 "output_name": "output_file2"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
708 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
709 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
710 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
711 "name": "extractseq",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
712 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
713 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
714 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
715 "type": "fasta"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
716 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
717 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
718 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
719 "left": 3656,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
720 "top": 1161.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
721 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
722 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
723 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
724 "tool_id": "extractseq",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
725 "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
726 "tool_version": "0.03",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
727 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
728 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
729 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
730 "23": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
731 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
732 "id": 23,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
733 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
734 "db_opts|histdb": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
735 "id": 9,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
736 "output_name": "outfile"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
737 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
738 "query": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
739 "id": 21,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
740 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
741 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
742 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
743 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
744 "name": "NCBI BLAST+ blastn",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
745 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
746 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
747 "name": "output1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
748 "type": "tabular"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
749 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
750 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
751 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
752 "left": 4008,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
753 "top": 956
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
754 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
755 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
756 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
757 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
758 "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
759 "tool_version": "0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
760 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
761 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
762 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
763 "24": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
764 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
765 "id": 24,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
766 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
767 "db_opts|histdb": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
768 "id": 9,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
769 "output_name": "outfile"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
770 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
771 "query": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
772 "id": 22,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
773 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
774 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
775 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
776 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
777 "name": "NCBI BLAST+ blastn",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
778 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
779 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
780 "name": "output1",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
781 "type": "tabular"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
782 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
783 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
784 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
785 "left": 4011,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
786 "top": 1117.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
787 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
788 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
789 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
790 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
791 "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
792 "tool_version": "0.1.00",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
793 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
794 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
795 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
796 "25": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
797 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
798 "id": 25,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
799 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
800 "input_blast_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
801 "id": 23,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
802 "output_name": "output1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
803 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
804 "input_variant_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
805 "id": 20,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
806 "output_name": "output_file1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
807 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
808 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
809 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
810 "name": "ParseBlastForUniqueMatch",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
811 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
812 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
813 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
814 "type": "pileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
815 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
816 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
817 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
818 "left": 4304,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
819 "top": 824
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
820 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
821 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
822 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
823 "tool_id": "ParseBlastForUniqueMatch",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
824 "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
825 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
826 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
827 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
828 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
829 "26": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
830 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
831 "id": 26,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
832 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
833 "input_blast_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
834 "id": 24,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
835 "output_name": "output1"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
836 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
837 "input_variant_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
838 "id": 20,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
839 "output_name": "output_file2"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
840 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
841 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
842 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
843 "name": "ParseBlastForUniqueMatch",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
844 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
845 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
846 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
847 "type": "pileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
848 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
849 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
850 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
851 "left": 4303.5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
852 "top": 1037.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
853 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
854 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
855 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
856 "tool_id": "ParseBlastForUniqueMatch",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
857 "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
858 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
859 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
860 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
861 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
862 "27": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
863 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
864 "id": 27,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
865 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
866 "input_file1": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
867 "id": 25,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
868 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
869 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
870 "input_file2": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
871 "id": 26,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
872 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
873 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
874 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
875 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
876 "name": "MergeFile2x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
877 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
878 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
879 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
880 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
881 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
882 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
883 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
884 "left": 4707,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
885 "top": 957.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
886 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
887 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
888 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
889 "tool_id": "MergeFile2x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
890 "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file1\": \"null\", \"input_file2\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
891 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
892 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
893 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
894 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
895 "28": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
896 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
897 "id": 28,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
898 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
899 "input_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
900 "id": 27,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
901 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
902 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
903 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
904 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
905 "name": "mpileupfilterandstat",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
906 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
907 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
908 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
909 "type": "pileup"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
910 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
911 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
912 "name": "log_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
913 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
914 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
915 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
916 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
917 "left": 5067,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
918 "top": 1011.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
919 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
920 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
921 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
922 "tool_id": "mpileupfilterandstat",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
923 "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
924 "tool_version": "0.08",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
925 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
926 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
927 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
928 "29": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
929 "annotation": "",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
930 "id": 29,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
931 "input_connections": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
932 "input_blast_filtered_part1_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
933 "id": 25,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
934 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
935 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
936 "input_blast_filtered_part2_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
937 "id": 26,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
938 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
939 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
940 "input_list_filtered_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
941 "id": 19,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
942 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
943 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
944 "input_mpileup_variant_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
945 "id": 18,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
946 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
947 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
948 "input_read1_part1_trimmed_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
949 "id": 7,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
950 "output_name": "output_read1_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
951 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
952 "input_read1_part2_trimmed_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
953 "id": 8,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
954 "output_name": "output_read1_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
955 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
956 "input_read1_row_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
957 "id": 0,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
958 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
959 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
960 "input_read2_part1_trimmed_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
961 "id": 7,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
962 "output_name": "output_read2_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
963 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
964 "input_read2_part2_trimmed_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
965 "id": 8,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
966 "output_name": "output_read2_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
967 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
968 "input_read2_row_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
969 "id": 1,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
970 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
971 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
972 "input_sam_filtered_part1_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
973 "id": 12,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
974 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
975 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
976 "input_sam_filtered_part2_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
977 "id": 13,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
978 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
979 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
980 "input_sam_row_part1_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
981 "id": 10,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
982 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
983 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
984 "input_sam_row_part2_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
985 "id": 11,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
986 "output_name": "output"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
987 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
988 "input_snp_selected_file": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
989 "id": 28,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
990 "output_name": "output_file"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
991 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
992 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
993 "inputs": [],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
994 "name": "rapsosnp_stats2x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
995 "outputs": [
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
996 {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
997 "name": "output_file",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
998 "type": "txt"
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
999 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1000 ],
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1001 "position": {
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1002 "left": 2133.5,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1003 "top": 165.5
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1004 },
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1005 "post_job_actions": {},
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1006 "tool_errors": null,
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1007 "tool_id": "rapsosnp_stats2x",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1008 "tool_state": "{\"input_blast_filtered_part1_file\": \"null\", \"input_blast_filtered_part2_file\": \"null\", \"input_sam_row_part2_file\": \"null\", \"input_read1_part1_trimmed_file\": \"null\", \"__page__\": 0, \"input_list_filtered_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_read2_row_file\": \"null\", \"input_mpileup_variant_file\": \"null\", \"input_read2_part1_trimmed_file\": \"null\", \"input_read1_row_file\": \"null\", \"input_sam_row_part1_file\": \"null\", \"input_sam_filtered_part2_file\": \"null\", \"input_read2_part2_trimmed_file\": \"null\", \"input_snp_selected_file\": \"null\", \"input_read1_part2_trimmed_file\": \"null\", \"input_sam_filtered_part1_file\": \"null\"}",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1009 "tool_version": "0.01",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1010 "type": "tool",
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1011 "user_outputs": []
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1012 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1013 }
9332b9da7491 Uploaded
mcharles
parents:
diff changeset
1014 }