Tuiuiu asynchronous workflow

Created: 2009-06-29 09:53:39 Last updated: 2009-06-29 09:59:23

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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 an asynchronous way: the workflow will launch Tuiuiu and then regularly poll the server for results.

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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 (9)

Name	Type	Description
launchJobOutputXML	local	This is the output of Tuiuiu webservice: status of the job, job output, ...
launchJobInputXML	local	This is where you define all the input data to Tuiuiu webservice.
launchJob	arbitrarywsdl	Requires all the parameters with correct type, and structures representing the input files. The structure contains the name of the input file and either the contents in Base64 encoded binary form or a MIME attachment, or simply a location (URL) to the associated file. The operation returns a Job ID that can be used to retrieve job status and outputs.
getOutputsOutputXML	local	These are the files generated by Tuiuiu.
outputFileXML	local	Every file used by Tuiuiu service will be represented by this outputFileXML object.
filterListOfStringsByRegex	local	A list of urls of input and output files used during this request to the Tuiuiu webservice.
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).
getOutputs	arbitrarywsdl	returns the outputs from a job that is identified by a Job ID. The output consists of the urls for the standard output and error, and an array of structures representing the output files. The structure contains the name of the output file and the url from where it can be downloaded.
PollStatus	workflow	This nested workflow is a loop which will regularly request the job status to the server until it is finished.

Beanshells (1)

Name	Description	Inputs	Outputs
IsFinished		code	isFinished

Outputs (1)

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

Links (18)

Source	Sink
dataOutputFileName	launchJobInputXML:dataOutputFileName
infoOutputFileName	launchJobInputXML:infoOutputFileName
inputFastaFileContent	inputFastaFileXML:contents
inputFastaFileName	inputFastaFileXML:name
inputFastaFileXML:output	launchJobInputXML:inputFastaFile
launchJobOutputXML:jobID	PollStatus:JobID
multiSequence	launchJobInputXML:multiSequence
regexOutputUrlFilter	filterListOfStringsByRegex:regex
launchJobInputXML:output	launchJob:launchJobInput
singleSequence	launchJobInputXML:singleSequence
useExcellentAlgorithm	launchJobInputXML:useExcellentAlgorithm
useGoodAlgorithm	launchJobInputXML:useGoodAlgorithm
filterListOfStringsByRegex:filteredlist	dataOutput
getOutputs:getOutputsOutput	getOutputsOutputXML:input
getOutputsOutputXML:outputFile	outputFileXML:input
launchJob:launchJobOutput	launchJobOutputXML:input
launchJobOutputXML:jobID	getOutputs:getOutputsInput
outputFileXML:url	filterListOfStringsByRegex:stringlist