Workflows

List files by regex - no matches (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_regex service. Since no files match the regular expression 'x.*' i.e. no files have a name that starts with 'x', an empty list is output.

Created: 2010-10-28

List files by regex - several answers (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_regex service and the file paths matching the regular expression '.*i.*', i.e. those containing an 'i', are output.

Created: 2010-10-28

List files by regex - single match (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_regex service and the file path to the one file matching 'c.*' i.e. starting with 'c' is output.

Created: 2010-10-28

Read text file - empty file (1)

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the empty string ''.

Created: 2010-10-28 | Last updated: 2010-10-28

Read text file (1)

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The beanshell write the string 'hello' to a temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the string 'hello'.

Created: 2010-10-28

Read text file - several lines (1)

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The beanshell write the string 'hello' four times separated by a new lineto a temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the string 'hello hello hello hello'.

Created: 2010-10-28

Write text file - empty string value (1)

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file service which writes the empty string '' into the file. '' is also output by the service.

Created: 2010-10-28

Write text file - overwriting content (1)

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file A service which writes the string 'hello' into the file. After service A has run, service B writes 'goodbye' into the file. The file is then read by the Read_Text_File service and its content, 'goodbye', output by the workflow.

Created: 2010-10-28

Write text file - specified value (1)

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file service which writes 'hello' into the file. 'hello' is also output by the service.

Created: 2010-10-28

Flatten list (1)

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The flatten_list service takes the list [['a'], ['b'], ['c'], ['d']] and outputs the list ['a', 'b', 'c', 'd', 'e'].

Created: 2010-10-28 | Last updated: 2010-10-28

Merge string list to string - colon separator (1)

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The merge string list to string service takes the list ['a','b','c'] and using the separator ':' outputs the string 'a:b:c'.

Created: 2010-10-28

Merge string list to a string - default se... (1)

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The merge string list to string service takes the list ['a','b','c'] and outputs the string 'a b c'.

Created: 2010-10-28

Merge string list to string - empty list (1)

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The merge string list to string service takes an empty list [] and outputs an empty string ''.

Created: 2010-10-28

Remove duplicate strings - empty list (1)

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The remove duplicate strings service takes the empty list [] and outputs the result [].

Created: 2010-10-29 | Last updated: 2010-10-29

Remove duplicate strings (1)

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The remove duplicate strings service takes the list ['a','b','c','b','a','d'], strips out duplicate strings and outputs the result ['a','b','c','d'].

Created: 2010-10-29

Get image from URL - only url specified (1)

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Retrieve the image at http://www.mygrid.org.uk/files/2008/09/dragon-workflow.png using just the url parameter

Created: 2010-10-29

Get image from URL - url and base specified (1)

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Retrieve the image at http://www.mygrid.org.uk/files/2008/09/dragon-workflow.png using both the url and base parameters

Created: 2010-10-29 | Last updated: 2010-10-29

Get image URLs from HTTP document - no images (1)

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Retrieve the web page at http://www.mygrid.org.uk/usermanual1.7/user_gettings_started.html and examine it for images. The workflow should return an empty list.

Created: 2010-10-29 | Last updated: 2010-10-29

Get image URLs from HTTP document and outp... (2)

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Retrieve the web page at http://www.mygrid.org.uk, examine it for images and output the images.

Created: 2010-10-29 | Last updated: 2014-02-12

Get web page from URL - just url (1)

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Fetches a web page from http://www.mygrid.org.uk/tools using just the url parameter of the service. Note that when viewed, the HTML may not be rendered correctly. However, the HTML may be viewed by rendering the result as plain text.

Created: 2010-10-29

Get web page from URL - url and base (1)

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Fetches a web page from http://www.mygrid.org.uk/tools with the base parameter as "http://www.mygrid.org.uk" and the url as "/tools". Note that when viewed, the HTML may not be rendered correctly. However, the HTML may be viewed by rendering the result as plain text.

Created: 2010-10-29 | Last updated: 2010-10-29

Always fails - no parameters (1)

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The always fails service generates a service failure when no parameter values are supplied.

Created: 2010-10-29 | Last updated: 2010-10-29

Always fails - one parameter (1)

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The always fails service generates a service failure when one parameter value is supplied.

Created: 2010-10-29 | Last updated: 2010-10-29

Always fails - two parameters (1)

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The always fails service generates a service failure when two parameter values are supplied.

Created: 2010-10-29 | Last updated: 2010-10-29

Echo_with_occasional_failure (1)

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The Sometimes_Fails service mostly echoes the string 'hello' to the out port. Sometimes, it throws a service failure.

Created: 2010-10-29 | Last updated: 2010-10-29

Byte Array to string - empty value (1)

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The beanshell converts the empty string '' to a byte array which is then converted back to the empty string '' by the Byte_Array_To_string service.

Created: 2010-10-29 | Last updated: 2010-10-29

Byte Array to string - non empty value (1)

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The beanshell converts the string 'hello' to a byte array which is then converted back to the string 'hello' by the Byte_Array_to_string service.

Created: 2010-10-29 | Last updated: 2010-10-29

Concatenate two strings - empty strings (1)

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The concatenate two strings service takes two empty strings and returns an empty string.

Created: 2010-10-29 | Last updated: 2010-10-29

Concatenate two strings (1)

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The concatenate two strings service takes the strings 'good' and 'bye' and returns the result 'goodbye'.

Created: 2010-10-29

FIlter list of strings by regex with a sui... (1)

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The workflow filters the five element list split from the first service and returns the three elements that match the regular expression.

Created: 2010-10-29

FIlter list of strings by regex with an un... (1)

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The workflow filters the five element list split from the first service and returns an empty list as no elements match.

Created: 2010-10-29

FIlter list of strings by regex extracting... (1)

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The workflow examines the five element list split from the first service. For each element, if it contains an 'a' followed by two characters, then the two characters after the 'a' are included in the output. Thus, for the input ['a','b','abcde','cdef','axy'], only 'abcde' and 'axy' contain a match and so ['bc', 'xy'] is output.

Created: 2010-10-29

FIlter list of strings by regex extracting... (1)

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The workflow examines the five element list split from the first service. For each element, if it contains an 'a' followed by two characters, then that triple is included in the output. Thus, for the input ['a','b','abcde','cdef','axy'], only 'abcde' and 'axy' contain a match and so ['abc', 'axy'] is output.

Created: 2010-10-29

Pad numeral with leading 0s - default targ... (1)

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The pad numeral with leading 0s takes the input '12' and pads it to the default target length of 7, yielding the output '0000012'.

Created: 2010-10-29 | Last updated: 2010-10-29

Pathways and Gene annotations for QTL region (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in rice, Oryza sativa. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniGene identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway d...

Created: 2011-05-27 | Last updated: 2011-05-27

Credits: Paul Fisher

Molecular Interactions from IntAct PSICQUI... (2)

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Get molecular interaction data in psi-mitab25 from IntAct through its REST PSICQUIC service. As input you can use an Uniprot Acc like "P99999" or a MIQL query like "alias:KHDRBS1".

Created: 2011-05-29 | Last updated: 2011-10-05

Credits: Rafael C. Jimenez

Find PRIDE experiments by GO (1)

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Find PRIDE experiments in Human with related information like Cell Type and Tissue location filtering results by Gene Ontology terms. This is an example of how to use the PRIDE Biomart service in Taverna. Many other options are possible by modifying the filters and attributes of this service.

Created: 2011-05-29 | Last updated: 2011-05-29

Credits: Rafael C. Jimenez

Find Reactome pathways and reactions by GO (1)

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Find Reactome pathways and reactions (names and accessions) in Human querying by a Gene Ontology term. This is an example of how to use the Reactome Biomart service in Taverna. Many other possibilities are possible by modifying the filters and attributes options of the service.

Created: 2011-05-29 | Last updated: 2011-05-29

Credits: Rafael C. Jimenez

Find Biological Models by GO. (1)

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Find Biological Models (Ids and Names) from Biomodels querying by Gene Ontology terms.

Created: 2011-05-29 | Last updated: 2011-05-29

Credits: Rafael C. Jimenez

DAS sequence retrieval (2)

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Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS).

Created: 2011-05-30 | Last updated: 2011-05-30

Credits: Rafael C. Jimenez

DAS sequence retrieval and parsing with JDAS (1)

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Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS) and create your own text output by modifying the JDAS component. To be able to use this workflow with JDAS, copy this file … http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar … to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs.

Created: 2011-05-30 | Last updated: 2011-05-30

Credits: Rafael C. Jimenez

DAS features retrieval (2)

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Retrieve Protein or Genome features (annotations) using the Distributed Annotation System (DAS).

Created: 2011-06-01 | Last updated: 2011-06-01

Credits: Rafael C. Jimenez

DAS features retrieval and parsing with JDAS (2)

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Retrieve Protein or Genome features using the Distributed Annotation System (DAS) and create your own text output by modifying the JDAS component. To be able to use this workflow with JDAS copy this file … http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar … to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs.

Created: 2011-06-01 | Last updated: 2011-06-02

Credits: Rafael C. Jimenez

blastn and blastx (1)

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This workflow accepts an url of a fasta file as input and performs an NCBI blastn at the EBI against the bacteria database and an NCBI blastx against the uniref90 database.  From the blast results of the blastx the hit with the lowest e-value is taken and the GO is returned. Output is blastx and blastn results and GO from the first hit of the blastx.   Based on Katy Wolstencroft & Hamish McWilliam EBI_NCBI_BLAST http://www.myexperiment.org/workflows/1765.html

Created: 2011-06-08 | Last updated: 2011-06-08

Credits: Niek

Retrieval of molecular interactions within... (1)

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Description of the flow steps: 1. split the list of identifiers using allows separators, 2. build a MIQL query with these identifier in preparation of running a PSICQUIC request, 3. Retrieve molecular interaction from IntAct's PSICQUIC service using the generated MIQL statement, 4. filter the list of returned MITAB using the list of identifiers and only keep those lines where both participating molecules are members of the input list, 5. return the count and list of filtered MITAB lines.

Created: 2011-06-10 | Last updated: 2011-06-10

Credits: Skerrien

Detect compressed TIFF files and remove th... (3)

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The workflow takes a list of TIFF images as input, identifies the "Group 4 Fax" comressed TIFF images and converts them to uncompressed TIFF images using convert. Finally it characterises the converted image. This version of the workflow replaces the web services of the original workflow with tool services.

Created: 2011-06-15 | Last updated: 2012-03-08

Credits: Sven

Attributions:

Extract histogram features from image file (1)

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As a template for creation of image workflows was used xa-toolwrapper project from Sven Schlarb (https://github.com/openplanets/scape/tree/master/xa-toolwrapper). This project enables creation of WSDL web service that wraps command line tool like ‘extractFeatures’ or ‘create’. The workflow for ‘extractFeatures’ tool has two input parameters. The URL to the input image file and the number of histogram bins as integer. This workflow extracts histogram feature...

Created: 2011-06-16 | Last updated: 2012-04-04

Credits: Roman

Compare histogram features of image files (1)

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As a template for creation of image workflows was used xa-toolwrapper project from Sven Schlarb (https://github.com/openplanets/scape/tree/master/xa-toolwrapper). This project enables creation of WSDL web service that wraps command line tool like ‘extractFeatures’ or ‘create’. The workflow for ‘compare’ tool has three input parameters. These are two URLs to the XML histogram files that comprise information about image features. These files are acquired us...

Created: 2011-06-16 | Last updated: 2012-04-04

Credits: Roman

[untitled] (1)

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This is simly a test fortest

Created: 2011-06-19 | Last updated: 2011-06-19

Credits: Merdmann

Associate hessi flares with active regions (3)

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This workflow is querying the HFC ActiveRegions list and HEC hessi_flare list. It requires a time periode and a search radius arround the centre of an Active Region as inputs It produces two outputs: AnnotatedFeatureTable is a modified VOTable where a field is added with the number of associated hessi flares. CombinedTable is a 2 dimensional list with an VOTable for each Active region and one with an VOTable for all associated flares for that Active Region.

Created: 2011-06-22 | Last updated: 2012-07-10

Credits: Donal Fellows