mobyle2.services/extractseq.yaml at master · mobyle2/mobyle2.services · GitHub

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
!mobyle/program
name: extractseq
title: extractseq
description: Extract regions from a sequence
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:2044']
    - !mobyle/inputprogramparagraph
        prompt: Required section
        name: required
        children:
        - !mobyle/inputprogramparameter
            comment: "Regions to extract. \n A set of regions is specified by a set\
                \ of pairs of positions. \n  The positions are integers. \n  They\
                \ are separated by any non-digit, non-alpha character. \n  Examples\
                \ of region specifications are: \n  24-45, 56-78 \n  1:45, 67=99;765..888\
                \ \n  1,5,8,10,23,45,57,99"
            prompt: 'Regions to extract (eg: 4-57,78-94)'
            format: ("", " -regions=" + str(value))[value is not None]
            simple: true
            argpos: 2
            mandatory: true
            name: regions
            command: false
            type: !mobyle/stringtype {}
    - !mobyle/inputprogramparagraph
        prompt: Additional section
        name: additional
        children:
        - !mobyle/inputprogramparameter
            comment: 'If this is set true then each specified region is written out
                as a separate sequence. The name of the sequence is created  from
                the name of the original sequence with the start and end  positions
                of the range appended with underscore characters between  them, eg:
                XYZ region 2 to 34 is written as: XYZ_2_34'
            prompt: Write regions to separate sequences
            format: ("", " -separate")[ bool(value) ]
            argpos: 3
            name: separate
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        prompt: Output section
        name: output
        children:
        - !mobyle/inputprogramparameter
            prompt: Name of the output sequence file (outseq)
            format: ("" , " -outseq=" + str(value))[value is not None]
            argpos: 4
            name: outseq
            command: false
            type: !mobyle/stringtype {default: extractseq.outseq}
        - !mobyle/inputprogramparameter
            prompt: Choose the sequence output format
            format: ("", " -osformat=" + str(value))[value is not None and value!=vdef]
            argpos: 5
            name: osformat_outseq
            command: false
            type: !mobyle/stringtype
                default: FASTA
                options:
                - {label: Embl, value: EMBL}
                - {label: Fasta, value: FASTA}
                - {label: Gcg, value: GCG}
                - {label: Genbank, value: GENBANK}
                - {label: Nbrf, value: NBRF}
                - {label: Pir, value: PIR}
                - {label: Raw, value: RAW}
                - {label: Swissprot, value: SWISSPROT}
    - !mobyle/inputprogramparameter
        prompt: Turn off any prompting
        format: '" -auto -stdout"'
        argpos: 6
        name: auto
        command: false
        hidden: true
        type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparagraph
        prompt: Output section
        name: output
        children:
        - !mobyle/outputprogramparameter
            prompt: Outseq_out option
            filenames: outseq
            name: outseq_out
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"extractseq.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"extractseq.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0369']
topics: ['EDAM_topic:0156']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/extractseq.html', 'http://emboss.sourceforge.net/docs/themes']
command: extractseq
env: {}