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Provider:
European Bioinformatics Institute (EMBL-EBI)
Location:
UNITED KINGDOM
Submitter/Source:
Mike Mayer (over 9 years ago)
Base URL:
http://www.ebi.ac.uk/soaplab/services/edit.trimseq
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/edit.trimseq?wsdl(download last cached WSDL file)
Documentation URL(s): None Login to add a documentation URL Description(s): No description(s) yet Login to add a description ELIXIR Description(s): No info yet Login to add an elixir description Details (from Soaplab server): from Soaplab server(over 8 years ago)
- ds_lsr_analysis :
- analysis :
- name : trimseq
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Edit
- description : Remove unwanted characters from start and end of sequence(s)
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : trimseq
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Edit
- description : Remove unwanted characters from start and end of 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
- list_item :
- list :
- base :
- range :
- format : %d
- max :
- min : 1
- repeatable :
- base :
- name : window
- ordering : 4
- option :
- name : EDAM:0001251
- type : normal
- value : data Window size
- name : calculated_hardmax
- type : normal
- value : ${sequence.length}
- name : scalemin
- type : style
- value : 1
- help : This determines the size of the region that is considered when deciding whether the percentage of ambiguity is greater than the threshold. A value of 5 means that a region of 5 letters in the sequence is shifted along the sequence from the ends and trimming is done only if there is a greater or equal percentage of ambiguity than the threshold percentage.
- default : 1
- qualifier : window
- mandatory : false
- prompt : Window size
- type : long
- range :
- format : %f
- repeatable :
- base :
- name : percent
- ordering : 5
- option :
- name : EDAM:0002146
- type : normal
- value : data Threshold
- help : This is the threshold of the percentage ambiguity in the window required in order to trim a sequence.
- default : 100.0
- qualifier : percent
- mandatory : false
- prompt : Percent threshold of ambiguity in window
- type : float
- base :
- name : strict
- ordering : 6
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : In nucleic sequences, trim off not only N’s and X’s, but also the nucleotide IUPAC ambiguity codes M, R, W, S, Y, K, V, H, D and B. In protein sequences, trim off not only X’s but also B and Z.
- default : false
- qualifier : strict
- mandatory : false
- prompt : Trim off all ambiguity codes, not just N or X
- type : boolean
- base :
- name : star
- ordering : 7
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : In protein sequences, trim off not only X’s, but also the *’s
- default : false
- qualifier : star
- mandatory : false
- prompt : Trim off asterisks
- type : boolean
- base :
- name : left
- ordering : 10
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- default : false
- qualifier : left
- mandatory : false
- prompt : Trim at the start
- type : boolean
- base :
- name : right
- ordering : 11
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- default : false
- qualifier : right
- mandatory : false
- prompt : Trim at the end
- type : boolean
- 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
- list_item :
- repeatable :
- list :
- base :
- data :
- option :
- name : EDAM:0000156
- type : normal
- value : topic Sequence editing
- name : EDAM:0000235
- type : normal
- value : operation Sequence ambiguity calculation
- name : EDAM:0000369
- type : normal
- value : operation Sequence cutting
- 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/trimseq.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : window
- default : 1
- mandatory : false
- type : long
- name : percent
- default : 100.0
- mandatory : false
- type : float
- name : strict
- default : false
- mandatory : false
- type : boolean
- name : star
- default : false
- mandatory : false
- type : boolean
- name : left
- default : false
- mandatory : false
- type : boolean
- name : right
- default : false
- mandatory : false
- type : boolean
- analysis :
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