Workflows

Fail if true - false value (1)

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The fail if true service executes without an exception if given the value 'false'.

Created: 2008-09-27

Credits: Alan Williams

Fail if false - non false value (1)

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The fail if true service executes without an exception if given a non-false value such as 'fred'.

Created: 2008-09-27

Credits: Alan Williams

Fail if false - true value (1)

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The fail if true service executes without an exception if given the value 'true'.

Created: 2008-09-27

Credits: Alan Williams

Create lots of strings (1)

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The create lots of strings service returns a list containing a large number of strings.

Created: 2008-09-27 | Last updated: 2008-09-27

Credits: Alan Williams

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: 2008-09-27

Credits: Alan Williams

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: 2008-09-27

Credits: Alan Williams

Concatenate files - multiple files (1)

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The workflow splits the string 'a,b,c,d,e' into its five elements and saves the individual strings to five temporary files. The file paths to those files are then output by the create_and_populate_temporary_file beanshell. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service concatenates the five files and writes the result to the temporary output file. Because the displayresults port has no value, the results are not...

Created: 2008-09-27

Credits: Alan Williams

Concatenate files - echo results but no files (1)

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The split_string_into_string_list_by_regular_expresson outputs an empty list since the string to be split is defaulted to ''. As there are no input values, the create_and_populate_temporary_file generates an empty list. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service does not write anything to the temporary output file. Because the displayresults port has been given a default value of 'true', the empty string is ...

Created: 2008-09-27

Credits: Alan Williams

Concatenate files - echo results and multi... (1)

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The workflow splits the string 'a,b,c,d,e' into its five elements and saves the individual strings to five temporary files. The file paths to those files are then output by the create_and_populate_temporary_file beanshell. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service concatenates the five files and writes the result to the temporary output file. Because the displayresults port has been given a default value of...

Created: 2008-09-27

Credits: Alan Williams

Choose - single element list (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a' and outputs the list ['a']. The choose service displays a dialog with 'Some title' and 'Some message'. The user is only able to choose the value 'a'. When the user presses OK 'a' is passed to the answer port of the choose service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Choose - title and message parameters (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The choose service displays a dialog with 'Some title' and with 'Some message'. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Choose - title parameter (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The choose service displays a dialog with 'Some title' but no message. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Choose - no title or message parameters (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The choose service displays a dialog with no title or message. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Byte[] 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[]_to_string service.

Created: 2008-09-27

Credits: Alan Williams

Byte[] 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[]_to_string service.

Created: 2008-09-27

Credits: Alan Williams

Ask - title and message parameters (1)

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The ask service displays a prompt with 'Some title' and the prompt message 'Some message'. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Ask - just message parameter (1)

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The ask service displays a prompt with no title but with the prompt message 'Some message'. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Ask - just title parameter (1)

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The ask service displays a prompt with the title 'Some title' but no prompt message. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Ask - no parameters (1)

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The ask service displays a prompt with no title and no prompt message. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

linking3.xml (1)

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This workflow links between a specified EMBL accesion number to corresponding identifiers in the MEDLINE database.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

metabolic.xml (1)

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An example of how a more complex workflow can federate multiple resources to perform data mining. In this case a single input data item in the form of a probe set identifier is cross referenced to data sets in multiple locations to answer a kind of 'show me everything about this data' question.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

gene_ontology_diagram.xml (1)

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This workflow builds up a subgraph of the Gene Ontology (http://www.geneontology.org) to show the context for a supplied term or terms. It shows this context by colouring all ancestors of the term, all children and all siblings. By default, ancestors of the supplied term or terms are coloured orange, siblings purple and direct children teal. Other terms appear in the default wheat colour.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

BlastComparer.xml (1)

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Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers. N.B. this workflow does not function correctly as it is designed for use with NCBI blast scripts. Some errors may occur. Please use two blast text file inputs for a secure result output.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

interpro_url.xml (1)

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An example of how a more complex workflow can federate multiple resources to perform data mining. In this case a single input data item in the form of a probe set identifier is cross referenced to data sets in multiple locations to answer a kind of 'show me everything about this data' question.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

Example of an alternate processor (1)

Trivial workflow which will initially fail, retry twice then fall over to the alternative specified for the FailingThing process.

Created: 2008-05-28

Credits: Jfogel