Mercurial > repos > crs4 > glimmer

comparison Galaxy-Workflow-Glimmer.ga @ 0:9c8ffce71f7c draft default tip

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Uploaded
author crs4
date Mon, 09 Sep 2013 12:16:17 -0400
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-1:000000000000 0:9c8ffce71f7c
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "glimmer-from-scratch",
4 "format-version": "0.1",
5 "name": "Glimmer",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "",
14 "name": "Genome sequence"
15 }
16 ],
17 "name": "Input dataset",
18 "outputs": [],
19 "position": {
20 "left": 158,
21 "top": 200
22 },
23 "tool_errors": null,
24 "tool_id": null,
25 "tool_state": "{\"name\": \"Genome sequence\"}",
26 "tool_version": null,
27 "type": "data_input",
28 "user_outputs": []
29 },
30 "1": {
31 "annotation": "",
32 "id": 1,
33 "input_connections": {
34 "loSequence": {
35 "id": 0,
36 "output_name": "output"
37 }
38 },
39 "inputs": [],
40 "name": "Long-ORFs",
41 "outputs": [
42 {
43 "name": "logfile",
44 "type": "txt"
45 },
46 {
47 "name": "loOutput",
48 "type": "glimmer_coords"
49 }
50 ],
51 "position": {
52 "left": 248,
53 "top": 336
54 },
55 "post_job_actions": {},
56 "tool_errors": null,
57 "tool_id": "long-orfs_wrapper",
58 "tool_state": "{\"loFixed\": \"\\\"False\\\"\", \"__page__\": 0, \"loMaxOverlap\": \"\\\"\\\"\", \"loMinLen\": \"\\\"\\\"\", \"loStartCodons\": \"\\\"\\\"\", \"loTransTable\": \"\\\"\\\"\", \"loNoHeader\": \"\\\"False\\\"\", \"loLengthOpt\": \"\\\"False\\\"\", \"loCutoff\": \"\\\"\\\"\", \"loStopCodons\": \"\\\"\\\"\", \"loLinear\": \"\\\"False\\\"\", \"loWithoutStops\": \"\\\"False\\\"\", \"loEntropy\": \"null\", \"loSequence\": \"null\"}",
59 "tool_version": "0.2",
60 "type": "tool",
61 "user_outputs": []
62 },
63 "2": {
64 "annotation": "",
65 "id": 2,
66 "input_connections": {
67 "exCoords": {
68 "id": 1,
69 "output_name": "loOutput"
70 },
71 "exSequence": {
72 "id": 0,
73 "output_name": "output"
74 }
75 },
76 "inputs": [],
77 "name": "Extract",
78 "outputs": [
79 {
80 "name": "logfile",
81 "type": "txt"
82 },
83 {
84 "name": "exOutput",
85 "type": "fasta"
86 }
87 ],
88 "position": {
89 "left": 659,
90 "top": 231
91 },
92 "post_job_actions": {},
93 "tool_errors": null,
94 "tool_id": "extract_wrapper",
95 "tool_state": "{\"__page__\": 0, \"exSequence\": \"null\", \"exCoords\": \"null\", \"exDir\": \"\\\"False\\\"\", \"exNoStop\": \"\\\"False\\\"\", \"exNoStart\": \"\\\"False\\\"\", \"exNoWrap\": \"\\\"False\\\"\", \"exMinLen\": \"\\\"\\\"\", \"ex2Fields\": \"\\\"False\\\"\"}",
96 "tool_version": "0.2",
97 "type": "tool",
98 "user_outputs": []
99 },
100 "3": {
101 "annotation": "",
102 "id": 3,
103 "input_connections": {
104 "biSequence": {
105 "id": 2,
106 "output_name": "exOutput"
107 }
108 },
109 "inputs": [],
110 "name": "Build-ICM",
111 "outputs": [
112 {
113 "name": "logfile",
114 "type": "txt"
115 },
116 {
117 "name": "biIcm",
118 "type": "glimmer_icm"
119 }
120 ],
121 "position": {
122 "left": 177,
123 "top": 715
124 },
125 "post_job_actions": {},
126 "tool_errors": null,
127 "tool_id": "build-icm_wrapper",
128 "tool_state": "{\"__page__\": 0, \"biStopCodons\": \"\\\"\\\"\", \"biPeriod\": \"\\\"3\\\"\", \"biTransTable\": \"\\\"\\\"\", \"biNoStops\": \"\\\"False\\\"\", \"biDepth\": \"\\\"7\\\"\", \"biReverse\": \"\\\"False\\\"\", \"biSequence\": \"null\", \"biWidth\": \"\\\"12\\\"\"}",
129 "tool_version": "0.2",
130 "type": "tool",
131 "user_outputs": []
132 },
133 "4": {
134 "annotation": "",
135 "id": 4,
136 "input_connections": {
137 "glIcm": {
138 "id": 3,
139 "output_name": "biIcm"
140 },
141 "glSequence": {
142 "id": 0,
143 "output_name": "output"
144 }
145 },
146 "inputs": [],
147 "name": "Glimmer3",
148 "outputs": [
149 {
150 "name": "logfile",
151 "type": "txt"
152 },
153 {
154 "name": "glDetail",
155 "type": "txt"
156 },
157 {
158 "name": "glPredict",
159 "type": "txt"
160 }
161 ],
162 "position": {
163 "left": 508,
164 "top": 715
165 },
166 "post_job_actions": {},
167 "tool_errors": null,
168 "tool_id": "glimmer3_wrapper",
169 "tool_state": "{\"__page__\": 0, \"glFirstCodon\": \"\\\"False\\\"\", \"glNoIndep\": \"\\\"False\\\"\", \"glIcm\": \"null\", \"glRbsPwm\": \"null\", \"glEntropy\": \"null\", \"glSeparateGenes\": \"\\\"False\\\"\", \"glOrfCoords\": \"null\", \"glMaxOverlap\": \"\\\"\\\"\", \"glIgnoreScoreLen\": \"\\\"\\\"\", \"glGcPercent\": \"\\\"\\\"\", \"glSequence\": \"null\", \"glGeneLen\": \"\\\"\\\"\", \"glStopCodons\": \"\\\"\\\"\", \"glExtend\": \"\\\"False\\\"\", \"glLinear\": \"\\\"False\\\"\", \"glTransTable\": \"\\\"\\\"\", \"glThreshold\": \"\\\"\\\"\", \"glStartCodons\": \"\\\"\\\"\", \"glStartProbs\": \"\\\"\\\"\"}",
170 "tool_version": "0.2",
171 "type": "tool",
172 "user_outputs": []
173 }
174 }
175 }