|
0
|
1 {
|
|
|
2 "a_galaxy_workflow": "true",
|
|
|
3 "annotation": "",
|
|
|
4 "format-version": "0.1",
|
|
|
5 "name": "Glimmer gene calling with trainingset.",
|
|
|
6 "steps": {
|
|
|
7 "0": {
|
|
|
8 "annotation": "The set of genes is used to train the gene calling of glimmer.",
|
|
|
9 "id": 0,
|
|
|
10 "input_connections": {},
|
|
|
11 "inputs": [
|
|
|
12 {
|
|
|
13 "description": "The set of genes is used to train the gene calling of glimmer.",
|
|
|
14 "name": "Set of Genes"
|
|
|
15 }
|
|
|
16 ],
|
|
|
17 "name": "Input dataset",
|
|
|
18 "outputs": [],
|
|
|
19 "position": {
|
|
|
20 "left": 283,
|
|
|
21 "top": 376
|
|
|
22 },
|
|
|
23 "tool_errors": null,
|
|
|
24 "tool_id": null,
|
|
|
25 "tool_state": "{\"name\": \"Set of Genes\"}",
|
|
|
26 "tool_version": null,
|
|
|
27 "type": "data_input",
|
|
|
28 "user_outputs": []
|
|
|
29 },
|
|
|
30 "1": {
|
|
|
31 "annotation": "",
|
|
|
32 "id": 1,
|
|
|
33 "input_connections": {},
|
|
|
34 "inputs": [
|
|
|
35 {
|
|
|
36 "description": "",
|
|
|
37 "name": "Input Genomic Sequence"
|
|
|
38 }
|
|
|
39 ],
|
|
|
40 "name": "Input dataset",
|
|
|
41 "outputs": [],
|
|
|
42 "position": {
|
|
|
43 "left": 443,
|
|
|
44 "top": 232
|
|
|
45 },
|
|
|
46 "tool_errors": null,
|
|
|
47 "tool_id": null,
|
|
|
48 "tool_state": "{\"name\": \"Input Genomic Sequence\"}",
|
|
|
49 "tool_version": null,
|
|
|
50 "type": "data_input",
|
|
|
51 "user_outputs": []
|
|
|
52 },
|
|
|
53 "2": {
|
|
|
54 "annotation": "",
|
|
|
55 "id": 2,
|
|
|
56 "input_connections": {
|
|
|
57 "infile": {
|
|
|
58 "id": 0,
|
|
|
59 "output_name": "output"
|
|
|
60 }
|
|
|
61 },
|
|
|
62 "inputs": [],
|
|
|
63 "name": "Glimmer ICM builder",
|
|
|
64 "outputs": [
|
|
|
65 {
|
|
|
66 "name": "outfile",
|
|
|
67 "type": "data"
|
|
|
68 }
|
|
|
69 ],
|
|
|
70 "position": {
|
|
|
71 "left": 503,
|
|
|
72 "top": 486
|
|
|
73 },
|
|
|
74 "post_job_actions": {},
|
|
|
75 "tool_errors": null,
|
|
|
76 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer/glimmer_build-icm/0.2",
|
|
|
77 "tool_state": "{\"__page__\": 0, \"depth\": \"\\\"7\\\"\", \"period\": \"\\\"3\\\"\", \"width\": \"\\\"12\\\"\", \"stop_codon_opts\": \"{\\\"genbank_gencode\\\": \\\"11\\\", \\\"__current_case__\\\": 0, \\\"stop_codon_opts_selector\\\": \\\"gb\\\"}\", \"no_stops\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/bag/projects/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"infile\": \"null\"}",
|
|
|
78 "tool_version": "0.2",
|
|
|
79 "type": "tool",
|
|
|
80 "user_outputs": []
|
|
|
81 },
|
|
|
82 "3": {
|
|
|
83 "annotation": "",
|
|
|
84 "id": 3,
|
|
|
85 "input_connections": {
|
|
|
86 "icm_input": {
|
|
|
87 "id": 2,
|
|
|
88 "output_name": "outfile"
|
|
|
89 },
|
|
|
90 "seq_input": {
|
|
|
91 "id": 1,
|
|
|
92 "output_name": "output"
|
|
|
93 }
|
|
|
94 },
|
|
|
95 "inputs": [],
|
|
|
96 "name": "Glimmer3",
|
|
|
97 "outputs": [
|
|
|
98 {
|
|
|
99 "name": "genes_output",
|
|
|
100 "type": "fasta"
|
|
|
101 },
|
|
|
102 {
|
|
|
103 "name": "report_output",
|
|
|
104 "type": "txt"
|
|
|
105 },
|
|
|
106 {
|
|
|
107 "name": "detailed_output",
|
|
|
108 "type": "txt"
|
|
|
109 }
|
|
|
110 ],
|
|
|
111 "position": {
|
|
|
112 "left": 674,
|
|
|
113 "top": 319
|
|
|
114 },
|
|
|
115 "post_job_actions": {},
|
|
|
116 "tool_errors": null,
|
|
|
117 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer/glimmer_knowlegde-based/0.2",
|
|
|
118 "tool_state": "{\"extend\": \"\\\"False\\\"\", \"__page__\": 0, \"linear\": \"\\\"True\\\"\", \"detailed_report\": \"\\\"False\\\"\", \"seq_input\": \"null\", \"gc_percent\": \"\\\"0.0\\\"\", \"start_codons\": \"\\\"atg,gtg,ttg\\\"\", \"threshold\": \"\\\"30\\\"\", \"stop_codon_opts\": \"{\\\"genbank_gencode\\\": \\\"11\\\", \\\"__current_case__\\\": 0, \\\"stop_codon_opts_selector\\\": \\\"gb\\\"}\", \"max_olap\": \"\\\"50\\\"\", \"no_indep\": \"\\\"False\\\"\", \"gene_len\": \"\\\"90\\\"\", \"report\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/bag/projects/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"icm_input\": \"null\"}",
|
|
|
119 "tool_version": "0.2",
|
|
|
120 "type": "tool",
|
|
|
121 "user_outputs": []
|
|
|
122 },
|
|
|
123 "4": {
|
|
|
124 "annotation": "",
|
|
|
125 "id": 4,
|
|
|
126 "input_connections": {
|
|
|
127 "input1": {
|
|
|
128 "id": 3,
|
|
|
129 "output_name": "genes_output"
|
|
|
130 }
|
|
|
131 },
|
|
|
132 "inputs": [],
|
|
|
133 "name": "transeq",
|
|
|
134 "outputs": [
|
|
|
135 {
|
|
|
136 "name": "out_file1",
|
|
|
137 "type": "fasta"
|
|
|
138 }
|
|
|
139 ],
|
|
|
140 "position": {
|
|
|
141 "left": 988,
|
|
|
142 "top": 351
|
|
|
143 },
|
|
|
144 "post_job_actions": {},
|
|
|
145 "tool_errors": null,
|
|
|
146 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0",
|
|
|
147 "tool_state": "{\"trim\": \"\\\"no\\\"\", \"__page__\": 0, \"input1\": \"null\", \"out_format1\": \"\\\"fasta\\\"\", \"frame\": \"\\\"1\\\"\", \"regions\": \"\\\"\\\"\", \"clean\": \"\\\"no\\\"\", \"table\": \"\\\"11\\\"\", \"alternative\": \"\\\"no\\\"\"}",
|
|
|
148 "tool_version": "5.0.0",
|
|
|
149 "type": "tool",
|
|
|
150 "user_outputs": []
|
|
|
151 }
|
|
|
152 }
|
|
|
153 }
|
