This repository has been archived by the owner on May 28, 2024. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 0
/
cpgplot.yaml
257 lines (257 loc) · 10.2 KB
/
cpgplot.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
!mobyle/program
name: cpgplot
title: cpgplot
description: Identify and plot CpG islands in nucleotide sequence(s)
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparagraph
prompt: Input section
name: input
children:
- !mobyle/inputprogramparameter
prompt: Sequence option
format: ("", " -sequence=" + str(value))[value is not None]
simple: true
argpos: 1
mandatory: true
name: sequence
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:1927', 'EDAM_format:2200', 'EDAM_format:1935',
'EDAM_format:1936', 'EDAM_format:1948', 'EDAM_format:1948', 'EDAM_format:1957',
'EDAM_format:2188']
data_terms: ['EDAM_data:2977']
- !mobyle/inputprogramparagraph
prompt: Required section
name: required
children:
- !mobyle/inputprogramparameter
comment: The percentage CG content and the Observed frequency of CG is
calculated within a window whose size is set by this parameter. The
window is moved down the sequence and these statistics are calculated
at each position that the window is moved to.
prompt: Window size (value greater than or equal to 1)
format: ("", " -window=" + str(value))[value is not None and value!=vdef]
simple: true
argpos: 2
mandatory: true
name: window
command: false
type: !mobyle/integertype {default: 100}
ctrls:
- message: Value greater than or equal to 1 is required
test:
value: {'#gte': '1'}
- !mobyle/inputprogramparameter
comment: This sets the minimum length that a CpG island has to be before
it is reported.
prompt: Minimum length of an island (value greater than or equal to 1)
format: ("", " -minlen=" + str(value))[value is not None and value!=vdef]
simple: true
argpos: 3
mandatory: true
name: minlen
command: false
type: !mobyle/integertype {default: 200}
ctrls:
- message: Value greater than or equal to 1 is required
test:
value: {'#gte': '1'}
- !mobyle/inputprogramparameter
comment: This sets the minimum average observed to expected ratio of C
plus G to CpG in a set of 10 windows that are required before a CpG
island is reported.
prompt: Minimum observed/expected (value from 0. to 10.)
format: ("", " -minoe=" + str(value))[value is not None and value!=vdef]
simple: true
argpos: 4
mandatory: true
name: minoe
command: false
type: !mobyle/floattype {default: 0.6}
ctrls:
- message: Value greater than or equal to 0. is required
test:
value: {'#gte': '0.0'}
- message: Value less than or equal to 10. is required
test:
value: {'#lte': '10.0'}
- !mobyle/inputprogramparameter
comment: This sets the minimum average percentage of G plus C a set of
10 windows that are required before a CpG island is reported.
prompt: Minimum percentage (value from 0. to 100.)
format: ("", " -minpc=" + str(value))[value is not None and value!=vdef]
simple: true
argpos: 5
mandatory: true
name: minpc
command: false
type: !mobyle/floattype {default: 50.0}
ctrls:
- message: Value greater than or equal to 0. is required
test:
value: {'#gte': '0.0'}
- message: Value less than or equal to 100. is required
test:
value: {'#lte': '100.0'}
- !mobyle/inputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/inputprogramparameter
comment: This sets the name of the file holding the report of the input
sequence name, CpG island parameters and the output details of any
CpG islands that are found.
prompt: Name of the output file (outfile)
format: ("" , " -outfile=" + str(value))[value is not None]
argpos: 6
name: outfile
command: false
type: !mobyle/stringtype {default: cpgplot.outfile}
- !mobyle/inputprogramparameter
prompt: Plot cpg island score
format: (" -noplot", "")[ bool(value) ]
argpos: 7
name: plot
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Choose the graph output format
format: (" -graph=" + str(vdef), " -graph=" + str(value))[value is not
None and value!=vdef]
argpos: 8
name: graph
precond: plot
command: false
type: !mobyle/stringtype
default: png
options:
- {label: Png, value: png}
- {label: Gif, value: gif}
- {label: Cps, value: cps}
- {label: Ps, value: ps}
- {label: Meta, value: meta}
- {label: Data, value: data}
- !mobyle/inputprogramparameter
prompt: Name of the output graph
format: ("" , " -goutfile=" + str(value))[value is not None]
argpos: 9
name: xy_goutfile
precond: plot
command: false
type: !mobyle/stringtype {default: cpgplot_xygraph}
- !mobyle/inputprogramparameter
comment: If this is set to true then the graph of the observed to expected
ratio of C plus G to CpG within a window is displayed.
prompt: Show observed/expected threshold line
format: (" -noobsexp", "")[ bool(value) ]
argpos: 10
name: obsexp
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: If this is set to true then the graph of the regions which have
been determined to be CpG islands is displayed.
prompt: Show cpg rich regions
format: (" -nocg", "")[ bool(value) ]
argpos: 11
name: cg
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: If this is set to true then the graph of the percentage C plus
G within a window is displayed.
prompt: Show percentage line
format: (" -nopc", "")[ bool(value) ]
argpos: 12
name: pc
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter {comment: File for output features, prompt: Name
of the output feature file (outfeat), format: '("" , " -outfeat="
+ str(value))[value is not None]', argpos: 13, name: outfeat, command: false}
- !mobyle/inputprogramparameter {prompt: Choose the feature output format,
format: '("", " -offormat=" + str(value))[value is not None and value!=vdef]',
argpos: 14, name: offormat_outfeat, command: false}
- !mobyle/inputprogramparameter
prompt: Turn off any prompting
format: '" -auto -stdout"'
argpos: 15
name: auto
command: false
hidden: true
type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/outputprogramparameter
prompt: Outfile_out option
filenames: outfile
name: outfile_out
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.png"'
name: xy_outgraph_png
precond:
'#and':
- plot
- {graph: png}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.gif"'
name: xy_outgraph_gif
precond:
'#and':
- plot
- {graph: gif}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.ps"'
name: xy_outgraph_ps
precond:
'#or':
- '#and':
- plot
- {graph: ps}
- {graph: cps}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.meta"'
name: xy_outgraph_meta
precond:
'#and':
- plot
- {graph: meta}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.dat"'
name: xy_outgraph_data
precond:
'#and':
- plot
- {graph: data}
- !mobyle/outputprogramparameter {prompt: Outfeat_out option, filenames: outfeat,
name: outfeat_out}
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"cpgplot.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"cpgplot.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0430', 'EDAM_operation:0576']
topics: ['EDAM_topic:0157']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/cpgplot.html', 'http://emboss.sourceforge.net/docs/themes']
command: cpgplot
env: {}