annotate rapsodyn/Galaxy-Workflow-rapsosnp_v1.20.ga @ 8:d857538d9fea draft

Uploaded
author mcharles
date Fri, 10 Oct 2014 07:05:36 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
d857538d9fea Uploaded
mcharles
parents:
diff changeset
1 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
2 "a_galaxy_workflow": "true",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
3 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
4 "format-version": "0.1",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
5 "name": "rapsosnp v1.20",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
6 "steps": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
7 "0": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
8 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
9 "id": 0,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
10 "input_connections": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
11 "inputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
12 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
13 "description": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
14 "name": "ASSEMBLY"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
15 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
16 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
17 "name": "Input dataset",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
18 "outputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
19 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
20 "left": 200,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
21 "top": 221
d857538d9fea Uploaded
mcharles
parents:
diff changeset
22 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
23 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
24 "tool_id": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
25 "tool_state": "{\"name\": \"ASSEMBLY\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
26 "tool_version": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
27 "type": "data_input",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
28 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
29 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
30 "1": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
31 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
32 "id": 1,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
33 "input_connections": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
34 "inputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
35 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
36 "description": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
37 "name": "READ1"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
38 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
39 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
40 "name": "Input dataset",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
41 "outputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
42 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
43 "left": 200,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
44 "top": 306.76666259765625
d857538d9fea Uploaded
mcharles
parents:
diff changeset
45 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
46 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
47 "tool_id": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
48 "tool_state": "{\"name\": \"READ1\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
49 "tool_version": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
50 "type": "data_input",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
51 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
52 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
53 "2": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
54 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
55 "id": 2,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
56 "input_connections": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
57 "inputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
58 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
59 "description": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
60 "name": "READ2"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
61 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
62 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
63 "name": "Input dataset",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
64 "outputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
65 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
66 "left": 200,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
67 "top": 392.5333251953125
d857538d9fea Uploaded
mcharles
parents:
diff changeset
68 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
69 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
70 "tool_id": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
71 "tool_state": "{\"name\": \"READ2\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
72 "tool_version": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
73 "type": "data_input",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
74 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
75 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
76 "3": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
77 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
78 "id": 3,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
79 "input_connections": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
80 "inputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
81 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
82 "description": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
83 "name": "DUBIOUS"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
84 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
85 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
86 "name": "Input dataset",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
87 "outputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
88 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
89 "left": 200,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
90 "top": 478.29998779296875
d857538d9fea Uploaded
mcharles
parents:
diff changeset
91 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
92 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
93 "tool_id": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
94 "tool_state": "{\"name\": \"DUBIOUS\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
95 "tool_version": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
96 "type": "data_input",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
97 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
98 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
99 "4": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
100 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
101 "id": 4,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
102 "input_connections": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
103 "input_fasta": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
104 "id": 0,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
105 "output_name": "output"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
106 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
107 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
108 "inputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
109 "name": "fastaGroomerForMakeBlastdb",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
110 "outputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
111 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
112 "name": "output_fasta",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
113 "type": "fasta"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
114 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
115 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
116 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
117 "left": 427.76666259765625,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
118 "top": 221
d857538d9fea Uploaded
mcharles
parents:
diff changeset
119 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
120 "post_job_actions": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
121 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
122 "tool_id": "fastaGroomerForMakeBlastdb",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
123 "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
124 "tool_version": "1.00",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
125 "type": "tool",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
126 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
127 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
128 "5": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
129 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
130 "id": 5,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
131 "input_connections": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
132 "input_read1_file": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
133 "id": 1,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
134 "output_name": "output"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
135 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
136 "input_read2_file": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
137 "id": 2,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
138 "output_name": "output"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
139 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
140 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
141 "inputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
142 "name": "PrepareFastqLight",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
143 "outputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
144 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
145 "name": "output_read1_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
146 "type": "fastqsanger"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
147 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
148 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
149 "name": "output_read2_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
150 "type": "fastqsanger"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
151 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
152 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
153 "name": "log_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
154 "type": "txt"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
155 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
156 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
157 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
158 "left": 427.76666259765625,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
159 "top": 351.76666259765625
d857538d9fea Uploaded
mcharles
parents:
diff changeset
160 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
161 "post_job_actions": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
162 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
163 "tool_id": "PrepareFastqLight",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
164 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"auto\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
165 "tool_version": "1.03",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
166 "type": "tool",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
167 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
168 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
169 "6": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
170 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
171 "id": 6,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
172 "input_connections": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
173 "input_file": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
174 "id": 4,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
175 "output_name": "output_fasta"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
176 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
177 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
178 "inputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
179 "name": "NCBI BLAST+ makeblastdb",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
180 "outputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
181 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
182 "name": "outfile",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
183 "type": "data"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
184 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
185 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
186 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
187 "left": 755.5333251953125,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
188 "top": 221
d857538d9fea Uploaded
mcharles
parents:
diff changeset
189 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
190 "post_job_actions": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
191 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
192 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
193 "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\\\"\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
194 "tool_version": "0.1.00",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
195 "type": "tool",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
196 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
197 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
198 "7": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
199 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
200 "id": 7,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
201 "input_connections": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
202 "genomeSource|ownFile": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
203 "id": 0,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
204 "output_name": "output"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
205 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
206 "paired|input1": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
207 "id": 5,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
208 "output_name": "output_read1_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
209 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
210 "paired|input2": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
211 "id": 5,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
212 "output_name": "output_read2_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
213 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
214 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
215 "inputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
216 "name": "Map with BWA for Illumina",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
217 "outputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
218 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
219 "name": "output",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
220 "type": "sam"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
221 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
222 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
223 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
224 "left": 755.5333251953125,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
225 "top": 378.76666259765625
d857538d9fea Uploaded
mcharles
parents:
diff changeset
226 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
227 "post_job_actions": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
228 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
229 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
230 "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\\\"\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
231 "tool_version": "1.2.3",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
232 "type": "tool",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
233 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
234 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
235 "8": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
236 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
237 "id": 8,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
238 "input_connections": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
239 "input_sam_file": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
240 "id": 7,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
241 "output_name": "output"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
242 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
243 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
244 "inputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
245 "name": "filtersam_mapped_and_unique",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
246 "outputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
247 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
248 "name": "output_sam_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
249 "type": "sam"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
250 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
251 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
252 "name": "log_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
253 "type": "txt"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
254 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
255 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
256 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
257 "left": 1083.300048828125,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
258 "top": 221
d857538d9fea Uploaded
mcharles
parents:
diff changeset
259 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
260 "post_job_actions": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
261 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
262 "tool_id": "filtersam_mapped_and_unique",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
263 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
264 "tool_version": "1.01",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
265 "type": "tool",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
266 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
267 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
268 "9": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
269 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
270 "id": 9,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
271 "input_connections": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
272 "source|input1": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
273 "id": 8,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
274 "output_name": "output_sam_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
275 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
276 "source|ref_file": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
277 "id": 0,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
278 "output_name": "output"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
279 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
280 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
281 "inputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
282 "name": "SAM-to-BAM",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
283 "outputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
284 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
285 "name": "output1",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
286 "type": "bam"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
287 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
288 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
289 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
290 "left": 1411.066650390625,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
291 "top": 221
d857538d9fea Uploaded
mcharles
parents:
diff changeset
292 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
293 "post_job_actions": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
294 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
295 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
296 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
297 "tool_version": "1.1.4",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
298 "type": "tool",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
299 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
300 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
301 "10": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
302 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
303 "id": 10,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
304 "input_connections": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
305 "reference_source|input_bams_0|input_bam": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
306 "id": 9,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
307 "output_name": "output1"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
308 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
309 "reference_source|ref_file": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
310 "id": 0,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
311 "output_name": "output"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
312 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
313 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
314 "inputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
315 "name": "MPileup",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
316 "outputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
317 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
318 "name": "output_mpileup",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
319 "type": "pileup"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
320 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
321 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
322 "name": "output_log",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
323 "type": "txt"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
324 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
325 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
326 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
327 "left": 1638.8333740234375,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
328 "top": 221
d857538d9fea Uploaded
mcharles
parents:
diff changeset
329 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
330 "post_job_actions": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
331 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
332 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
333 "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\\\": \\\"0\\\", \\\"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}\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
334 "tool_version": "0.0.3",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
335 "type": "tool",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
336 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
337 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
338 "11": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
339 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
340 "id": 11,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
341 "input_connections": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
342 "input_pileup_file": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
343 "id": 10,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
344 "output_name": "output_mpileup"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
345 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
346 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
347 "inputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
348 "name": "PileupVariant",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
349 "outputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
350 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
351 "name": "output_pileup_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
352 "type": "pileup"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
353 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
354 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
355 "name": "log_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
356 "type": "txt"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
357 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
358 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
359 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
360 "left": 1964.60009765625,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
361 "top": 221
d857538d9fea Uploaded
mcharles
parents:
diff changeset
362 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
363 "post_job_actions": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
364 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
365 "tool_id": "PileupVariant",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
366 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_pileup_file\": \"null\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
367 "tool_version": "1.01",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
368 "type": "tool",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
369 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
370 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
371 "12": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
372 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
373 "id": 12,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
374 "input_connections": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
375 "input_list1": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
376 "id": 11,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
377 "output_name": "output_pileup_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
378 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
379 "input_list2": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
380 "id": 3,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
381 "output_name": "output"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
382 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
383 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
384 "inputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
385 "name": "listfiltering",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
386 "outputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
387 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
388 "name": "output_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
389 "type": "pileup"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
390 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
391 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
392 "name": "log_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
393 "type": "txt"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
394 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
395 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
396 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
397 "left": 2292.36669921875,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
398 "top": 221
d857538d9fea Uploaded
mcharles
parents:
diff changeset
399 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
400 "post_job_actions": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
401 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
402 "tool_id": "listfiltering",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
403 "tool_state": "{\"__page__\": 0, \"input_list2\": \"null\", \"input_list1\": \"null\", \"__rerun_remap_job_id__\": null, \"nb_col\": \"\\\"2\\\"\", \"type\": \"\\\"specific\\\"\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
404 "tool_version": "1.01",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
405 "type": "tool",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
406 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
407 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
408 "13": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
409 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
410 "id": 13,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
411 "input_connections": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
412 "input_assembly_file": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
413 "id": 0,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
414 "output_name": "output"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
415 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
416 "input_variant_file": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
417 "id": 12,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
418 "output_name": "output_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
419 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
420 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
421 "inputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
422 "name": "extractseq",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
423 "outputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
424 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
425 "name": "output_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
426 "type": "fasta"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
427 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
428 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
429 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
430 "left": 2561.13330078125,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
431 "top": 221
d857538d9fea Uploaded
mcharles
parents:
diff changeset
432 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
433 "post_job_actions": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
434 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
435 "tool_id": "extractseq",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
436 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
437 "tool_version": "1.01",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
438 "type": "tool",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
439 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
440 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
441 "14": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
442 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
443 "id": 14,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
444 "input_connections": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
445 "db_opts|histdb": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
446 "id": 6,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
447 "output_name": "outfile"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
448 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
449 "query": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
450 "id": 13,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
451 "output_name": "output_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
452 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
453 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
454 "inputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
455 "name": "NCBI BLAST+ blastn",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
456 "outputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
457 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
458 "name": "output1",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
459 "type": "tabular"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
460 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
461 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
462 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
463 "left": 2888.89990234375,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
464 "top": 221
d857538d9fea Uploaded
mcharles
parents:
diff changeset
465 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
466 "post_job_actions": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
467 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
468 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
469 "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\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
470 "tool_version": "0.1.00",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
471 "type": "tool",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
472 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
473 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
474 "15": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
475 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
476 "id": 15,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
477 "input_connections": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
478 "input_blast_file": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
479 "id": 14,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
480 "output_name": "output1"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
481 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
482 "input_variant_file": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
483 "id": 12,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
484 "output_name": "output_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
485 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
486 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
487 "inputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
488 "name": "ParseBlastForUniqueMatch",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
489 "outputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
490 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
491 "name": "output_variant_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
492 "type": "pileup"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
493 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
494 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
495 "name": "log_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
496 "type": "txt"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
497 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
498 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
499 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
500 "left": 3190.666748046875,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
501 "top": 221
d857538d9fea Uploaded
mcharles
parents:
diff changeset
502 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
503 "post_job_actions": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
504 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
505 "tool_id": "ParseBlastForUniqueMatch",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
506 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
507 "tool_version": "1.01",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
508 "type": "tool",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
509 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
510 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
511 "16": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
512 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
513 "id": 16,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
514 "input_connections": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
515 "input_file": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
516 "id": 15,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
517 "output_name": "output_variant_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
518 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
519 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
520 "inputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
521 "name": "mpileupfilterandstat",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
522 "outputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
523 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
524 "name": "output_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
525 "type": "pileup"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
526 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
527 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
528 "name": "log_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
529 "type": "txt"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
530 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
531 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
532 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
533 "left": 3518.433349609375,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
534 "top": 221
d857538d9fea Uploaded
mcharles
parents:
diff changeset
535 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
536 "post_job_actions": {},
d857538d9fea Uploaded
mcharles
parents:
diff changeset
537 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
538 "tool_id": "mpileupfilterandstat",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
539 "tool_state": "{\"__page__\": 0, \"stat\": \"{\\\"stat_dist_step\\\": \\\"50\\\", \\\"stat_min_depth_step\\\": \\\"4\\\", \\\"stat_max_depth_max\\\": \\\"200\\\", \\\"stat_min_depth_max\\\": \\\"20\\\", \\\"stat_freq_max\\\": \\\"1.0\\\", \\\"stat_min_depth_min\\\": \\\"4\\\", \\\"stat_max_depth_min\\\": \\\"200\\\", \\\"do_stat\\\": \\\"YES\\\", \\\"stat_dist_min\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"stat_max_depth_step\\\": \\\"100\\\", \\\"stat_dist_max\\\": \\\"50\\\", \\\"stat_freq_step\\\": \\\"0.2\\\", \\\"stat_freq_min\\\": \\\"0.8\\\"}\", \"input_file\": \"null\", \"min_frequency\": \"\\\"0.0\\\"\", \"min_depth\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"500\\\"\", \"min_distance\": \"\\\"0\\\"\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
540 "tool_version": "1.00",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
541 "type": "tool",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
542 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
543 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
544 "17": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
545 "annotation": "",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
546 "id": 17,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
547 "input_connections": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
548 "input_files": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
549 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
550 "id": 5,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
551 "output_name": "log_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
552 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
553 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
554 "id": 8,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
555 "output_name": "log_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
556 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
557 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
558 "id": 11,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
559 "output_name": "log_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
560 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
561 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
562 "id": 12,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
563 "output_name": "log_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
564 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
565 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
566 "id": 15,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
567 "output_name": "log_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
568 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
569 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
570 "id": 16,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
571 "output_name": "log_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
572 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
573 ]
d857538d9fea Uploaded
mcharles
parents:
diff changeset
574 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
575 "inputs": [],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
576 "name": "MergeMultiFile",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
577 "outputs": [
d857538d9fea Uploaded
mcharles
parents:
diff changeset
578 {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
579 "name": "output_file",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
580 "type": "txt"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
581 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
582 ],
d857538d9fea Uploaded
mcharles
parents:
diff changeset
583 "position": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
584 "left": 3846.2001953125,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
585 "top": 221
d857538d9fea Uploaded
mcharles
parents:
diff changeset
586 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
587 "post_job_actions": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
588 "RenameDatasetActionoutput_file": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
589 "action_arguments": {
d857538d9fea Uploaded
mcharles
parents:
diff changeset
590 "newname": "LOGS"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
591 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
592 "action_type": "RenameDatasetAction",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
593 "output_name": "output_file"
d857538d9fea Uploaded
mcharles
parents:
diff changeset
594 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
595 },
d857538d9fea Uploaded
mcharles
parents:
diff changeset
596 "tool_errors": null,
d857538d9fea Uploaded
mcharles
parents:
diff changeset
597 "tool_id": "MergeMultiFile",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
598 "tool_state": "{\"out_format\": \"\\\"txt\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_files\": \"null\"}",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
599 "tool_version": "1.00",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
600 "type": "tool",
d857538d9fea Uploaded
mcharles
parents:
diff changeset
601 "user_outputs": []
d857538d9fea Uploaded
mcharles
parents:
diff changeset
602 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
603 }
d857538d9fea Uploaded
mcharles
parents:
diff changeset
604 }