Tuiuiu synchronous workflow

Created: 2009-06-29 09:42:08 Last updated: 2009-06-29 09:59:57

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Tuiuiu removes from a sequence or from a set of sequences areas as large as possible that do not contain researched repeats.

Tuiuiu is used as a preliminary step before applying a multiple local aligner tool.

Modeling and algorithmic details are provided in the following paper.
Please, cite this paper if you use Tuiuiu.

P. Peterlongo, G. Sacomoto, A. Pereira do Lago, N. Pisanti, M.-F. Sagot
Lossless filter for multiple repeats with bounded edit distance
BMC Algorithms for Molecular Biology 2009, 4:3 doi:10.1186/1748-7188-4-3

Link: http://www.almob.org/content/4/1/3

This web service is made available on GenOuest bioinformatics platform (Rennes, France) using Opal toolkit. A list of other web-services available on GenOuest platform can be viewed here.

This workflow uses Tuiuiu in a synchronous way: the workflow will launch Tuiuiu and wait the end of the job before continuing.

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Workflow Components

Inputs (9)

Name	Description
inputFastaFileName	Give a name to the input fasta file.
inputFastaFileContent	Load input fasta data from a file on your hard drive.
useGoodAlgorithm	'true' or 'false': use the algorithm which gives good results and is faster. Set useExcellentAlgorithm to the opposite value.
useExcellentAlgorithm	'true' or 'false': use the algorithm which gives excellent results but is slower. Set useGoodAlgorithm to the opposite value.
singleSequence	'true' or 'false': search for repeats in a unique sequence. Set multiSequence to the opposite value.
multiSequence	'true' or 'false': search for repeats in a set of sequences. Set singleSequence to the opposite value.
dataOutputFileName	Choose a name for the data output file (the file containing filtered sequence in fasta format).
infoOutputFileName	Choose a name for the information output file (the file providing informations about: Input data, parameters used, Positions conserved - between '[' and ']' -, Computations informations (Size and percentage kept by Tuiuiu, execution time)).
regexOutputUrlFilter	This is a regex to retrieve specific output file urls (if dataOutputFileName was set to 'data.out', then you can retrieve its url with a regex like 'data.*'). This is only a cosmetic thing to filter results sent by Tuiuiu webservice.

Processors (7)

Name	Type	Description
filterListOfStringsByRegex	local	This is a cosmetic filter which allow to only retrieve some of the output file urls sent by Tuiuiu service.
launchJobBlockingOutputXML	local	This is the output of Tuiuiu webservice: status of the job, job output, ...
outputFileXML	local	Every file used by Tuiuiu service will be represented by this outputFileXML object.
launchJobBlockingInputXML	local	This is where you define all the input data to Tuiuiu webservice.
jobOutXML	local	These are the files generated by Tuiuiu.
inputFastaFileXML	local	This object represent the input fasta file to send to Tuiuiu. There are three ways to send an input file. In each case, you first have to define a 'name' for the file. Then you can directly add file content by filling 'contents' value. Or you can give an URL where the input file can be downloaded. Or you can also attach the input file using SOAP attachment (more complex).
launchJobBlocking	arbitrarywsdl	Same as launchJob but blocks until the remote execution is complete, and returns job outputs (as described above) as the response. This operation may only be appropriate for jobs that are not long running.

Beanshells (0)

Outputs (1)

Name	Description
dataOutput	A list of urls of input and output files used during this request to the Tuiuiu webservice.

Links (16)

Source	Sink
dataOutputFileName	launchJobBlockingInputXML:dataOutputFileName
infoOutputFileName	launchJobBlockingInputXML:infoOutputFileName
inputFastaFileContent	inputFastaFileXML:contents
inputFastaFileName	inputFastaFileXML:name
multiSequence	launchJobBlockingInputXML:multiSequence
regexOutputUrlFilter	filterListOfStringsByRegex:regex
singleSequence	launchJobBlockingInputXML:singleSequence
useExcellentAlgorithm	launchJobBlockingInputXML:useExcellentAlgorithm
useGoodAlgorithm	launchJobBlockingInputXML:useGoodAlgorithm
inputFastaFileXML:output	launchJobBlockingInputXML:inputFastaFile
jobOutXML:outputFile	outputFileXML:input
launchJobBlocking:launchJobBlockingOutput	launchJobBlockingOutputXML:input
launchJobBlockingInputXML:output	launchJobBlocking:launchJobBlockingInput
launchJobBlockingOutputXML:jobOut	jobOutXML:input
outputFileXML:url	filterListOfStringsByRegex:stringlist
filterListOfStringsByRegex:filteredlist	dataOutput

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Tuiuiu synchronous workflow

Created by http://osallou.myopenid.com/ on Monday 29 June 2009 09:42:08 (UTC)

Last edited by http://osallou.myopenid.com/ on Monday 29 June 2009 09:59:58 (UTC)

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Tuiuiu removes from a sequence or from a set of sequences areas as large as possible that do not contain researched repeats. Tuiuiu is used as a preliminary step before applying a multiple local aligner tool. Modeling and algorithmic details are provided in the following paper. Please, cite this paper if you use Tuiuiu. P. Peterlongo, G. Sacomoto, A. Pereira do Lago, N. Pisanti, M.-F. Sagot Lossless filter for multiple repeats with bounded edit distance BMC Algorithms for Mole...

Created: 2009-06-29 | Last updated: 2009-06-29

Credits: http://osallou.myopenid.com/ GenOUEST Platform