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extractfeat.yaml
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extractfeat.yaml
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!mobyle/program
name: extractfeat
title: extractfeat
description: Extract features from 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:2044']
- !mobyle/inputprogramparagraph
prompt: Additional section
name: additional
children:
- !mobyle/inputprogramparameter
comment: If this value is greater than 0 then that number of bases or
residues before the feature are included in the extracted sequence.
This allows you to get the context of the feature. If this value
is negative then the start of the extracted sequence will be this
number of bases/residues before the end of the feature. So a value
of '10' will start the extraction 10 bases/residues before the start
of the sequence, and a value of '-10' will start the extraction 10
bases/residues before the end of the feature. The output sequence
will be padded with 'N' or 'X' characters if the sequence starts
after the required start of the extraction.
prompt: Amount of sequence before feature to extract
format: ("", " -before=" + str(value))[value is not None and value!=vdef]
argpos: 2
name: before
command: false
type: !mobyle/integertype {default: 0}
- !mobyle/inputprogramparameter
comment: If this value is greater than 0 then that number of bases or
residues after the feature are included in the extracted sequence.
This allows you to get the context of the feature. If this value
is negative then the end of the extracted sequence will be this number
of bases/residues after the start of the feature. So a value of '10'
will end the extraction 10 bases/residues after the end of the sequence,
and a value of '-10' will end the extraction 10 bases/residues after
the start of the feature. The output sequence will be padded with
'N' or 'X' characters if the sequence ends before the required end
of the extraction.
prompt: Amount of sequence after feature to extract
format: ("", " -after=" + str(value))[value is not None and value!=vdef]
argpos: 3
name: after
command: false
type: !mobyle/integertype {default: 0}
- !mobyle/inputprogramparameter
comment: "By default any feature source in the feature table is shown.\
\ You can set this to match any feature source you wish to show.\
\ \n The source name is usually either the name of the program that\
\ detected the feature or it is the feature table (eg: EMBL) that\
\ the feature came from. \n The source may be wildcarded by using\
\ '*'. \n If you wish to show more than one source, separate their\
\ names with the character '|', eg: \n gene* | embl"
prompt: Source of feature to display
format: ("", " -source=" + str(value))[value is not None]
argpos: 4
name: source
command: false
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
comment: "By default every feature in the feature table is extracted.\
\ You can set this to be any feature type you wish to extract. \n\
\ See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL \
\ feature types and see the Uniprot user manual in http://www.uniprot.org/manual/sequence_annotation\
\ for a list of the Uniprot feature types. \n The type may be wildcarded\
\ by using '*'. \n If you wish to extract more than one type, separate\
\ their names with the character '|', eg: \n *UTR | intron"
prompt: Type of feature to extract
format: ("", " -type=" + str(value))[value is not None]
argpos: 5
name: type
command: false
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
comment: By default any feature type in the feature table is extracted.
You can set this to match any feature sense you wish. 0 - any sense,
1 - forward sense, -1 - reverse sense
prompt: Sense of feature to extract
format: ("", " -sense=" + str(value))[value is not None and value!=vdef]
argpos: 6
name: sense
command: false
type: !mobyle/integertype {default: 0}
- !mobyle/inputprogramparameter
comment: Minimum score of feature to extract (see also maxscore)
prompt: Minimum score of feature to extract
format: ("", " -minscore=" + str(value))[value is not None and value!=vdef]
argpos: 7
name: minscore
command: false
type: !mobyle/floattype {default: 0.0}
- !mobyle/inputprogramparameter
comment: "Maximum score of feature to extract. \n If both minscore and\
\ maxscore are zero (the default), then any score is ignored"
prompt: Maximum score of feature to extract
format: ("", " -maxscore=" + str(value))[value is not None and value!=vdef]
argpos: 8
name: maxscore
command: false
type: !mobyle/floattype {default: 0.0}
- !mobyle/inputprogramparameter
comment: "Tags are the types of extra values that a feature may have.\
\ For example in the EMBL feature table, a 'CDS' type of feature \
\ may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number',\
\ '/evidence', '/exception', '/function', '/gene', '/label', '/map',\
\ '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo',\
\ '/standard_name', '/translation', '/transl_except', '/transl_table',\
\ or '/usedin'. Some of these tags also have values, for example\
\ '/gene' can have the value of the gene name. \n By default any\
\ feature tag in the feature table is extracted. You can set this\
\ to match any feature tag you wish to show. \n The tag may be wildcarded\
\ by using '*'. \n If you wish to extract more than one tag, separate\
\ their names with the character '|', eg: \n gene | label"
prompt: Tag of feature to extract
format: ("", " -tag=" + str(value))[value is not None]
argpos: 9
name: tag
command: false
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
comment: "Tag values are the values associated with a feature tag. Tags\
\ are the types of extra values that a feature may have. For example\
\ in the EMBL feature table, a 'CDS' type of feature may have the\
\ tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence',\
\ '/exception', '/function', '/gene', '/label', '/map', '/note',\
\ '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name',\
\ '/translation', '/transl_except', '/transl_table', or '/usedin'.\
\ Only some of these tags can have values, for example '/gene' can\
\ have the value of the gene name. By default any feature tag value\
\ in the feature table is shown. You can set this to match any feature\
\ tag value you wish to show. \n The tag value may be wildcarded\
\ by using '*'. \n If you wish to show more than one tag value, separate\
\ their names with a space or the character '|', eg: \n pax* | 10"
prompt: Value of feature tags to extract
format: ("", " -value=" + str(value))[value is not None]
argpos: 10
name: value
command: false
type: !mobyle/stringtype {}
- !mobyle/inputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/inputprogramparameter
comment: Some features, such as CDS (coding sequence) and mRNA are composed
of introns concatenated together. There may be other forms of 'joined'
sequence, depending on the feature table. If this option is set TRUE,
then any group of these features will be output as a single sequence.
If the 'before' and 'after' qualifiers have been set, then only the
sequence before the first feature and after the last feature are
added.
prompt: Output introns etc. as one sequence
format: ("", " -join")[ bool(value) ]
argpos: 11
name: join
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: To aid you in identifying the type of feature that has been output,
the type of feature is added to the start of the description of the
output sequence. Sometimes the description of a sequence is lost
in subsequent processing of the sequences file, so it is useful for
the type to be a part of the sequence ID name. If you set this to
be TRUE then the name is added to the ID name of the output sequence.
prompt: Append type of feature to output sequence name
format: ("", " -featinname")[ bool(value) ]
argpos: 12
name: featinname
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: "To aid you in identifying some further properties of a feature\
\ that has been output, this lets you specify one or more tag names\
\ that should be added to the output sequence Description text, together\
\ with their values (if any). For example, if this is set to be 'gene',\
\ then if any output feature has the tag (for example) '/gene=BRCA1'\
\ associated with it, then the text '(gene=BRCA1)' will be added\
\ to the Description line. Tags are the types of extra values that\
\ a feature may have. For example in the EMBL feature table, a 'CDS'\
\ type of feature may have the tags '/codon', '/codon_start', '/db_xref',\
\ '/EC_number', '/evidence', '/exception', '/function', '/gene',\
\ '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id',\
\ '/pseudo', '/standard_name', '/translation', '/transl_except',\
\ '/transl_table', or '/usedin'. Some of these tags also have values,\
\ for example '/gene' can have the value of the gene name. \n By\
\ default no feature tag is displayed. You can set this to match \
\ any feature tag you wish to show. \n The tag may be wildcarded\
\ by using '*'. \n If you wish to extract more than one tag, separate\
\ their names with the character '|', eg: \n gene | label"
prompt: Feature tag names to add to the description
format: ("", " -describe=" + str(value))[value is not None]
argpos: 13
name: describe
command: false
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
prompt: Name of the output sequence file (outseq)
format: ("" , " -outseq=" + str(value))[value is not None]
argpos: 14
name: outseq
command: false
type: !mobyle/stringtype {default: extractfeat.outseq}
- !mobyle/inputprogramparameter
prompt: Choose the sequence output format
format: ("", " -osformat=" + str(value))[value is not None and value!=vdef]
argpos: 15
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: 16
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: '"extractfeat.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"extractfeat.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0254']
topics: ['EDAM_topic:0160', 'EDAM_topic:0220']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/extractfeat.html', 'http://emboss.sourceforge.net/docs/themes']
command: extractfeat
env: {}