annotate Galaxy-Workflow-Differential_expression_DESeq.ga @ 6:59cc55f611f6 draft

Uploaded
author yufei-luo
date Tue, 22 Jan 2013 10:46:42 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
1 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
2 "a_galaxy_workflow": "true",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
3 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
4 "format-version": "0.1",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
5 "name": "Differential_expression_DESeq (with replicates)",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
6 "steps": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
7 "0": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
8 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
9 "id": 0,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
10 "input_connections": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
11 "inputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
12 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
13 "description": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
14 "name": "annotation.gff"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
15 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
16 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
17 "name": "Input dataset",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
18 "outputs": [],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
19 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
20 "left": 230,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
21 "top": 194.4166717529297
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
22 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
23 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
24 "tool_id": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
25 "tool_state": "{\"name\": \"annotation.gff\"}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
26 "tool_version": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
27 "type": "data_input",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
28 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
29 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
30 "1": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
31 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
32 "id": 1,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
33 "input_connections": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
34 "inputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
35 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
36 "description": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
37 "name": "Input replicat 1 for condition 1, fastq format"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
38 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
39 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
40 "name": "Input dataset",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
41 "outputs": [],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
42 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
43 "left": 229.9166717529297,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
44 "top": 260.41668701171875
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
45 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
46 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
47 "tool_id": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
48 "tool_state": "{\"name\": \"Input replicat 1 for condition 1, fastq format\"}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
49 "tool_version": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
50 "type": "data_input",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
51 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
52 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
53 "2": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
54 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
55 "id": 2,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
56 "input_connections": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
57 "inputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
58 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
59 "description": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
60 "name": "Input replicat 2 for condition 1, fastq format"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
61 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
62 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
63 "name": "Input dataset",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
64 "outputs": [],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
65 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
66 "left": 222.9166717529297,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
67 "top": 316.41668701171875
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
68 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
69 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
70 "tool_id": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
71 "tool_state": "{\"name\": \"Input replicat 2 for condition 1, fastq format\"}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
72 "tool_version": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
73 "type": "data_input",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
74 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
75 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
76 "3": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
77 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
78 "id": 3,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
79 "input_connections": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
80 "inputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
81 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
82 "description": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
83 "name": "Input replicat 1 for condition 2, fastq format"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
84 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
85 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
86 "name": "Input dataset",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
87 "outputs": [],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
88 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
89 "left": 222.9166717529297,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
90 "top": 380.41668701171875
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
91 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
92 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
93 "tool_id": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
94 "tool_state": "{\"name\": \"Input replicat 1 for condition 2, fastq format\"}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
95 "tool_version": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
96 "type": "data_input",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
97 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
98 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
99 "4": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
100 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
101 "id": 4,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
102 "input_connections": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
103 "inputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
104 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
105 "description": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
106 "name": "Input replicat 2 for condition 2, fastq format"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
107 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
108 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
109 "name": "Input dataset",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
110 "outputs": [],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
111 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
112 "left": 223.9166717529297,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
113 "top": 445.41668701171875
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
114 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
115 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
116 "tool_id": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
117 "tool_state": "{\"name\": \"Input replicat 2 for condition 2, fastq format\"}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
118 "tool_version": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
119 "type": "data_input",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
120 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
121 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
122 "5": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
123 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
124 "id": 5,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
125 "input_connections": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
126 "inputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
127 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
128 "description": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
129 "name": "Input replicat 3 for condition 2, fastq format"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
130 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
131 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
132 "name": "Input dataset",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
133 "outputs": [],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
134 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
135 "left": 222.9166717529297,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
136 "top": 511.41668701171875
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
137 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
138 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
139 "tool_id": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
140 "tool_state": "{\"name\": \"Input replicat 3 for condition 2, fastq format\"}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
141 "tool_version": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
142 "type": "data_input",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
143 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
144 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
145 "6": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
146 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
147 "id": 6,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
148 "input_connections": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
149 "inputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
150 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
151 "description": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
152 "name": "reference genome .fasta"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
153 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
154 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
155 "name": "Input dataset",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
156 "outputs": [],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
157 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
158 "left": 233.0833282470703,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
159 "top": 599
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
160 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
161 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
162 "tool_id": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
163 "tool_state": "{\"name\": \"reference genome .fasta\"}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
164 "tool_version": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
165 "type": "data_input",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
166 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
167 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
168 "7": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
169 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
170 "id": 7,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
171 "input_connections": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
172 "inputFile": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
173 "id": 0,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
174 "output_name": "output"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
175 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
176 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
177 "inputs": [],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
178 "name": "change gff Features",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
179 "outputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
180 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
181 "name": "outputFile",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
182 "type": "gff3"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
183 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
184 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
185 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
186 "left": 468.5,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
187 "top": 198
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
188 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
189 "post_job_actions": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
190 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
191 "tool_id": "changeGffFeatures",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
192 "tool_state": "{\"__page__\": 0, \"inputFeature\": \"\\\"gene\\\"\", \"outputFeature\": \"\\\"exon\\\"\", \"inputFile\": \"null\"}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
193 "tool_version": "1.0.0",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
194 "type": "tool",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
195 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
196 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
197 "8": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
198 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
199 "id": 8,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
200 "input_connections": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
201 "condition_groups_0|replicates_0|fastq_file": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
202 "id": 1,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
203 "output_name": "output"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
204 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
205 "condition_groups_0|replicates_1|fastq_file": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
206 "id": 2,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
207 "output_name": "output"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
208 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
209 "condition_groups_1|replicates_0|fastq_file": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
210 "id": 3,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
211 "output_name": "output"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
212 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
213 "condition_groups_1|replicates_1|fastq_file": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
214 "id": 4,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
215 "output_name": "output"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
216 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
217 "condition_groups_1|replicates_2|fastq_file": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
218 "id": 5,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
219 "output_name": "output"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
220 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
221 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
222 "inputs": [],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
223 "name": "load_multiFASTQfiles",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
224 "outputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
225 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
226 "name": "multiFASTQfiles_out",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
227 "type": "txt"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
228 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
229 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
230 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
231 "left": 434.16668701171875,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
232 "top": 312
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
233 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
234 "post_job_actions": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
235 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
236 "tool_id": "load_multiFASTQ",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
237 "tool_state": "{\"__page__\": 0, \"condition_groups\": \"[{\\\"__index__\\\": 0, \\\"replicates\\\": [{\\\"__index__\\\": 0, \\\"fastq_file\\\": null}, {\\\"__index__\\\": 1, \\\"fastq_file\\\": null}]}, {\\\"__index__\\\": 1, \\\"replicates\\\": [{\\\"__index__\\\": 0, \\\"fastq_file\\\": null}, {\\\"__index__\\\": 1, \\\"fastq_file\\\": null}, {\\\"__index__\\\": 2, \\\"fastq_file\\\": null}]}]\"}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
238 "tool_version": "1.0.0",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
239 "type": "tool",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
240 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
241 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
242 "9": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
243 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
244 "id": 9,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
245 "input_connections": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
246 "formatType|inputFileName": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
247 "id": 7,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
248 "output_name": "outputFile"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
249 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
250 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
251 "inputs": [],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
252 "name": "Clean Transcript File",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
253 "outputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
254 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
255 "name": "outputFile",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
256 "type": "gtf"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
257 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
258 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
259 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
260 "left": 696.4166870117188,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
261 "top": 255.41668701171875
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
262 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
263 "post_job_actions": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
264 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
265 "tool_id": "CleanTranscriptFile",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
266 "tool_state": "{\"optionType\": \"{\\\"type\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 0, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"__page__\": 0}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
267 "tool_version": "1.0.0",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
268 "type": "tool",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
269 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
270 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
271 "10": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
272 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
273 "id": 10,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
274 "input_connections": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
275 "input_file": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
276 "id": 8,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
277 "output_name": "multiFASTQfiles_out"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
278 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
279 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
280 "inputs": [],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
281 "name": "FASTQ Groomer parallel",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
282 "outputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
283 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
284 "name": "output_file",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
285 "type": "txt"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
286 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
287 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
288 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
289 "left": 692.5,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
290 "top": 351.41668701171875
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
291 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
292 "post_job_actions": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
293 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
294 "tool_id": "fastq_groomer_parallel",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
295 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"illumina\\\"\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
296 "tool_version": "1.0.0",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
297 "type": "tool",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
298 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
299 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
300 "11": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
301 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
302 "id": 11,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
303 "input_connections": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
304 "input1": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
305 "id": 10,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
306 "output_name": "output_file"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
307 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
308 "refGenomeSource|ownFile": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
309 "id": 6,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
310 "output_name": "output"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
311 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
312 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
313 "inputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
314 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
315 "description": "runtime parameter for tool Tophat parallel for Illumina",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
316 "name": "tar"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
317 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
318 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
319 "name": "Tophat parallel for Illumina",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
320 "outputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
321 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
322 "name": "outputFileName",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
323 "type": "txt"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
324 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
325 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
326 "name": "outputTarFile",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
327 "type": "tar"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
328 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
329 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
330 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
331 "left": 666.1666870117188,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
332 "top": 450
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
333 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
334 "post_job_actions": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
335 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
336 "tool_id": "tophat_parallel",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
337 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"tar\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"singlePaired\": \"{\\\"sParams\\\": {\\\"sSettingsType\\\": \\\"preSet\\\", \\\"__current_case__\\\": 0}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
338 "tool_version": "1.0.0",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
339 "type": "tool",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
340 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
341 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
342 "12": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
343 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
344 "id": 12,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
345 "input_connections": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
346 "input1": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
347 "id": 11,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
348 "output_name": "outputFileName"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
349 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
350 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
351 "inputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
352 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
353 "description": "runtime parameter for tool BAM to SAM",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
354 "name": "header"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
355 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
356 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
357 "description": "runtime parameter for tool BAM to SAM",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
358 "name": "tar"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
359 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
360 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
361 "name": "BAM to SAM",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
362 "outputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
363 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
364 "name": "output1",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
365 "type": "txt"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
366 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
367 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
368 "name": "outputTarFile",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
369 "type": "tar"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
370 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
371 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
372 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
373 "left": 927.1666870117188,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
374 "top": 473
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
375 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
376 "post_job_actions": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
377 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
378 "tool_id": "bam_to_sam_parallel",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
379 "tool_state": "{\"header\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input1\": \"null\", \"tar\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
380 "tool_version": "1.0.0",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
381 "type": "tool",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
382 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
383 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
384 "13": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
385 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
386 "id": 13,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
387 "input_connections": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
388 "formatType|inputFileName1": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
389 "id": 9,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
390 "output_name": "outputFile"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
391 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
392 "inputTxt": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
393 "id": 12,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
394 "output_name": "output1"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
395 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
396 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
397 "inputs": [],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
398 "name": "CompareOverlapping_parallel",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
399 "outputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
400 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
401 "name": "outTxtFile",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
402 "type": "txt"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
403 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
404 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
405 "name": "outputTarFile",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
406 "type": "tar"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
407 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
408 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
409 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
410 "left": 897.5,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
411 "top": 314.41668701171875
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
412 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
413 "post_job_actions": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
414 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
415 "tool_id": "CompareOverlapping_parallel",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
416 "tool_state": "{\"__page__\": 0, \"NotOverlapping\": \"\\\"True\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 1}\", \"InvertMatch\": \"\\\"False\\\"\", \"tar\": \"\\\"False\\\"\", \"ReportIntron\": \"\\\"False\\\"\", \"optionNFirstFile1\": \"{\\\"NFirstForFile1\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"optionExtentionTroisFile2\": \"{\\\"extentionFile2\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"optionExtentionTroisFile1\": \"{\\\"__current_case__\\\": 1, \\\"extentionFile1\\\": \\\"No\\\"}\", \"inputTxt\": \"null\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"optionExtentionCinqFile2\": \"{\\\"extentionFile2\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"MO\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"optionExtentionCinqFile1\": \"{\\\"__current_case__\\\": 1, \\\"extentionFile1\\\": \\\"No\\\"}\", \"OptionColinearOrAntiSens\": \"{\\\"__current_case__\\\": 2, \\\"OptionCA\\\": \\\"NONE\\\"}\", \"format2\": \"\\\"sam\\\"\", \"optionNFirstFile2\": \"{\\\"NFirstForFile2\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"optionNLastFile2\": \"{\\\"NLastForFile2\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"optionNLastFile1\": \"{\\\"__current_case__\\\": 1, \\\"NLastForFile1\\\": \\\"No\\\"}\"}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
417 "tool_version": "1.0.0",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
418 "type": "tool",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
419 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
420 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
421 "14": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
422 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
423 "id": 14,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
424 "input_connections": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
425 "inputTxt": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
426 "id": 13,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
427 "output_name": "outTxtFile"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
428 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
429 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
430 "inputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
431 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
432 "description": "runtime parameter for tool countNumber_parallel",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
433 "name": "tar"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
434 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
435 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
436 "name": "countNumber_parallel",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
437 "outputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
438 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
439 "name": "outputTxt",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
440 "type": "txt"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
441 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
442 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
443 "name": "outputTarFile",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
444 "type": "tar"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
445 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
446 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
447 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
448 "left": 1172.5833740234375,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
449 "top": 381
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
450 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
451 "post_job_actions": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
452 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
453 "tool_id": "countNumber_parallel",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
454 "tool_state": "{\"input\": \"null\", \"inputTxt\": \"null\", \"tar\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
455 "tool_version": "1.0.0",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
456 "type": "tool",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
457 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
458 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
459 "15": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
460 "annotation": "",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
461 "id": 15,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
462 "input_connections": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
463 "inputFile": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
464 "id": 14,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
465 "output_name": "outputTxt"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
466 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
467 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
468 "inputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
469 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
470 "description": "runtime parameter for tool DESEQ for differential expression analysis",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
471 "name": "withOutReplicates"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
472 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
473 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
474 "name": "DESEQ for differential expression analysis",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
475 "outputs": [
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
476 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
477 "name": "outHTML",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
478 "type": "HTML"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
479 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
480 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
481 "name": "outComplete",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
482 "type": "tabular"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
483 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
484 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
485 "name": "outUP",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
486 "type": "tabular"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
487 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
488 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
489 "name": "outDown",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
490 "type": "tabular"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
491 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
492 {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
493 "name": "log",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
494 "type": "txt"
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
495 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
496 ],
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
497 "position": {
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
498 "left": 1435.0833740234375,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
499 "top": 350
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
500 },
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
501 "post_job_actions": {},
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
502 "tool_errors": null,
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
503 "tool_id": "DESEQ",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
504 "tool_state": "{\"__page__\": 0, \"header\": \"\\\"True\\\"\", \"withOutReplicates\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"inputFile\": \"null\"}",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
505 "tool_version": "1.0.0",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
506 "type": "tool",
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
507 "user_outputs": []
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
508 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
509 }
59cc55f611f6 Uploaded
yufei-luo
parents:
diff changeset
510 }