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Soaplab server
(over 8 years ago)
- ds_lsr_analysis :
- analysis :
- name : extractfeat
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Edit, Feature tables
- description : Extract features from sequence(s)
- analysis_extension :
- input :
Show all
- ds_lsr_analysis :
- analysis :
- name : extractfeat
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Edit, Feature tables
- description : Extract features from sequence(s)
- analysis_extension :
- parameter :
- data :
- list :
- list_item :
- level : 0
- value : abi
- level : 0
- value : ace
- level : 0
- value : acedb
- level : 0
- value : bam
- level : 0
- value : biomart
- level : 0
- value : clustal
- level : 0
- value : codata
- level : 0
- value : dbid
- level : 0
- value : embl
- level : 0
- value : ensembl
- level : 0
- value : experiment
- level : 0
- value : fasta
- level : 0
- value : fastq
- level : 0
- value : fastq-illumina
- level : 0
- value : fastq-sanger
- level : 0
- value : fastq-solexa
- level : 0
- value : fitch
- level : 0
- value : gcg
- level : 0
- value : genbank
- level : 0
- value : genpept
- level : 0
- value : gff2
- level : 0
- value : gff3
- level : 0
- value : gifasta
- level : 0
- value : hennig86
- level : 0
- value : ig
- level : 0
- value : igstrict
- level : 0
- value : jackknifer
- level : 0
- value : mase
- level : 0
- value : mega
- level : 0
- value : msf
- level : 0
- value : nbrf
- level : 0
- value : nexus
- level : 0
- value : pdb
- level : 0
- value : pdbnuc
- level : 0
- value : pdbnucseq
- level : 0
- value : pdbseq
- level : 0
- value : pearson
- level : 0
- value : phylip
- level : 0
- value : phylipnon
- level : 0
- value : raw
- level : 0
- value : refseqp
- level : 0
- value : sam
- level : 0
- value : selex
- level : 0
- value : staden
- level : 0
- value : stockholm
- level : 0
- value : strider
- level : 0
- value : swiss
- level : 0
- value : text
- level : 0
- value : treecon
- type : full
- base :
- range :
- format : %d
- repeatable :
- base :
- name : before
- ordering : 4
- option :
- name : EDAM:0001249
- type : normal
- value : data Sequence length
- help : 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.
- default : 0
- qualifier : before
- mandatory : false
- prompt : Amount of sequence before feature to extract
- type : long
- range :
- format : %d
- repeatable :
- base :
- name : after
- ordering : 5
- option :
- name : EDAM:0001249
- type : normal
- value : data Sequence length
- help : 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.
- default : 0
- qualifier : after
- mandatory : false
- prompt : Amount of sequence after feature to extract
- type : long
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- range :
- format : %d
- repeatable :
- base :
- name : sense
- ordering : 8
- option :
- name : EDAM:0000853
- type : normal
- value : data DNA sense specification
- help : 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
- default : 0
- qualifier : sense
- mandatory : false
- prompt : Sense of feature to extract
- type : long
- range :
- format : %f
- repeatable :
- base :
- name : minscore
- ordering : 9
- option :
- name : EDAM:0001772
- type : normal
- value : data Score
- help : Minimum score of feature to extract (see also maxscore)
- default : 0.0
- qualifier : minscore
- mandatory : false
- prompt : Minimum score of feature to extract
- type : float
- range :
- format : %f
- repeatable :
- base :
- name : maxscore
- ordering : 10
- option :
- name : EDAM:0001772
- type : normal
- value : data Score
- help : Maximum score of feature to extract. If both minscore and maxscore are zero (the default), then any score is ignored
- default : 0.0
- qualifier : maxscore
- mandatory : false
- prompt : Maximum score of feature to extract
- type : float
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- base :
- name : join
- ordering : 15
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : 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.
- default : false
- qualifier : join
- mandatory : false
- prompt : Output introns etc. as one sequence
- type : boolean
- base :
- name : featinname
- ordering : 16
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : 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.
- default : false
- qualifier : featinname
- mandatory : false
- prompt : Append type of feature to output sequence name
- type : boolean
- standard :
- repeatable :
- base :
- data :
- result :
- iotype : output
- base :
- standard :
- list :
- list_item :
- level : 0
- value : acedb
- level : 0
- value : asn1
- level : 0
- value : bam
- level : 0
- value : clustal
- level : 0
- value : codata
- level : 0
- value : das
- level : 0
- value : dasdna
- level : 0
- value : embl
- level : 0
- value : experiment
- level : 0
- value : fasta
- level : 0
- value : fastq-illumina
- level : 0
- value : fastq-sanger
- level : 0
- value : fastq-solexa
- level : 0
- value : fitch
- level : 0
- value : gcg
- level : 0
- value : genbank
- level : 0
- value : genpept
- level : 0
- value : gff2
- level : 0
- value : gff3
- level : 0
- value : gifasta
- level : 0
- value : hennig86
- level : 0
- value : ig
- level : 0
- value : jackknifer
- level : 0
- value : jackknifernon
- level : 0
- value : mase
- level : 0
- value : mega
- level : 0
- value : meganon
- level : 0
- value : msf
- level : 0
- value : nbrf
- level : 0
- value : ncbi
- level : 0
- value : nexus
- level : 0
- value : nexusnon
- level : 0
- value : phylip
- level : 0
- value : phylipnon
- level : 0
- value : pir
- level : 0
- value : raw
- level : 0
- value : refseq
- level : 0
- value : refseqp
- level : 0
- value : sam
- level : 0
- value : selex
- level : 0
- value : staden
- level : 0
- value : strider
- level : 0
- value : swiss
- level : 0
- value : text
- level : 0
- value : treecon
- type : full
- repeatable :
- base :
- option :
- name : EDAM:0000160
- type : normal
- value : topic Sequence features
- name : EDAM:0000220
- type : normal
- value : topic File handling
- name : EDAM:0000254
- type : normal
- value : operation Sequence feature table extraction
- name : emboss
- type : normal
- value : true
- name : installation
- type : normal
- value : Soaplab2 default installation
- name : version
- type : normal
- value : 6.3.0
- app_info :
- category : edit
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/extractfeat.html
- event :
- action :
- id : _E_1
- input :
- name : before
- default : 0
- mandatory : false
- type : long
- name : after
- default : 0
- mandatory : false
- type : long
- name : sense
- default : 0
- mandatory : false
- type : long
- name : minscore
- default : 0.0
- mandatory : false
- type : float
- name : maxscore
- default : 0.0
- mandatory : false
- type : float
- name : join
- default : false
- mandatory : false
- type : boolean
- name : featinname
- default : false
- mandatory : false
- type : boolean
