Workflows

omim and pathways (2)

• Download

This workflow searches OMIM for entries associated with a particular disease in OMIM, returns the IDs and maps them to Kegg Gene IDs. For each gene, it then gets the description and any corresponding pathways those genes are involved with

Created: 2009-03-03 | Last updated: 2009-11-02

Credits: Katy Wolstencroft Paul Fisher

Attributions: Get Kegg Gene information

Example of a conditional execution workflow (1)

• Download

If the input is true then the string 'foo' is emited, if false then 'bar'. Just a simple example to show how the monster works, so to speak.

Created: 2008-10-06

Credits: hong nguyen

Extract elements from a list - extraction ... (1)

• Download

The extract_elements_from_a_list is passed the list [['a','b','c', 'd'], ['e','f','g','h'],['i','j','k','l'],['m','n','o','p']] with fromIndex of 1 and toIndex of 3 and depth 2, will output the list [['e','f','g','h'],['i','j','k','l']] as it is the outermost list i.e. that with depth 2 that is considered.

Created: 2008-09-29

Credits: Alan Williams

Extract elements from a list - extraction ... (1)

• Download

The extract_elements_from_a_list is passed the list [['a','b','c', 'd'], ['e','f','g','h'],['i','j','k','l'],['m','n','o','p']] with fromIndex of 1 and toIndex of 3 and the default depth of 1, will output the list [['b','c'], ['f','g'],['j','k'],['n','o'']] as it is the list with depth 1 e.g. ['e','f','g','h'] that are considered.

Created: 2008-09-29

Credits: Alan Williams

Flatten list - three depth (2)

• Download

The flatten_list service takes the list [[['a']], [['b']], [['c']], [['d']],[['e']]] and, using a flatten depth of 3, outputs the list ['a', 'b', 'c', 'd','e'].

Created: 2008-09-29 | Last updated: 2008-09-30

Credits: Alan Williams

Flatten list - two depth (1)

• Download

The flatten_list service takes the list [[['a']], [['b']], [['c']], [['d']]] and, using the default flatten depth of 2, outputs the list [['a'], ['b'], ['c'], ['d'], ['e']].

Created: 2008-09-29

Credits: Alan Williams

Echo_with_occasional_failure-1 (1)

• Download

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

Created: 2008-09-29

Credits: Alan Williams

Write text file - overwriting content (1)

• Download

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: 2008-09-27

Credits: Alan Williams

Write text file - empty string value (1)

• Download

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: 2008-09-27

Credits: Alan Williams

Write text file - specified value (1)

• Download

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: 2008-09-27

Credits: Alan Williams

Warn - title and message parameters (1)

• Download

The warn service displays a warning dialog with 'Some title' and message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Transform XML - output file by extension (1)

• Download

The get_xml_file_from_web service downloads an example xml from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xml_file. The path to the temporary file is passed to the inFileURL port of Transform_XML. The get_xslt_file_from_web service downloads an example xslt file from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xslt_file. The path to the temporary file is passed to the xslFileURL port...

Created: 2008-09-27

Credits: Alan Williams

Transform XML - no output file (1)

• Download

The get_xml_file_from_web service downloads an example xml from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xml_file. The path to the temporary file is passed to the inFileURL port of Transform_XML. The get_xslt_file_from_web service downloads an example xslt file from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xslt_file. The path to the temporary file is passed to the xslFileURL port...

Created: 2008-09-27

Credits: Alan Williams

Transcribe DNA (1)

• Download

The Transcribe DNA service takes the DNA sequence, here defaulted to 'gatcctccat' and outputs the corresponding transcribed RNA sequence, in this example, 'gauccuccau'.

Created: 2008-09-27

Credits: Alan Williams

Tell - title and message parameters (1)

• Download

The tell service displays an informative dialog with no title but with message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

String list union - yielding empty list (1)

• Download

The string list union service takes in two empty lists [] and [] and returns an empty list [].

Created: 2008-09-27

Credits: Alan Williams

String list union - yielding non-empty list (1)

• Download

The string list union service takes in ['a','b','c'] and ['a','e','c'] and returns a list equivalent to ['a','b','c','e'].

Created: 2008-09-27

Credits: Alan Williams

String list intersection - yielding empty ... (1)

• Download

The string list intersection service takes in ['a','b','c'] and ['x','y','z'] and returns the empty list [].

Created: 2008-09-27

Credits: Alan Williams

String list intersection - yielding non em... (1)

• Download

The string list intersection service takes in ['a','b','c'] and ['a','e','c] and returns the list ['a','c'].

Created: 2008-09-27

Credits: Alan Williams

String list difference - yielding empty list (1)

• Download

The string list difference service takes in ['a','b','c'] and ['a','c','b'] and returns the empty list [].

Created: 2008-09-27

Credits: Alan Williams

Split string into string list by regular e... (1)

• Download

The split string into string list by regular expression takes the string 'a,b,c' and using the default regular expression ',' splits it into the list ['a','b','c']

Created: 2008-09-27

Credits: Alan Williams

Select - single element list (1)

• Download

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

Created: 2008-09-27

Credits: Alan Williams

Select - title parameter (1)

• Download

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 select service displays a dialog with 'Some title' but no message. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

Created: 2008-09-27

Credits: Alan Williams

Select - no title or message parameters (1)

• Download

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 select service displays a dialog with no title or message. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

Created: 2008-09-27

Credits: Alan Williams

Remove duplicate strings - empty list (1)

• Download

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

Created: 2008-09-27

Credits: Alan Williams

Remove duplicate strings (1)

• Download

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: 2008-09-27

Credits: Alan Williams

Read text file - empty file (1)

• Download

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: 2008-09-27

Credits: Alan Williams

Read text file - several lines (1)

• Download

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: 2008-09-27

Credits: Alan Williams

Read text file (1)

• Download

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: 2008-09-27

Credits: Alan Williams

Read SwissProt file (1)

• Download

The Get_web_page_from_URL downloads a file from myExperiment that contains SwissProt data. That data is then saved to a temporary file generated by the create_and_populate_temporary_file beanshell. The path to the temporary file is then passed to the Read_SwissProt_file service. That service reads the file and converts the SwissProt data into Agave format. The result is then sent to the workflow's out port.

Created: 2008-09-27

Credits: Alan Williams

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

• Download

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: 2008-09-27

Credits: Alan Williams

Merge string list to string - empty list (1)

• Download

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

Created: 2008-09-27

Credits: Alan Williams

Merge string list to string - default sepa... (1)

• Download

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

Created: 2008-09-27

Credits: Alan Williams

List files by regex - empty directory (1)

• Download

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The empty directory is examined by the List_files_by_regex service. Since there are no files, an empty list is output.

Created: 2008-09-27

Credits: Alan Williams

List files by regex - no answer (1)

• Download

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: 2008-09-27

Credits: Alan Williams

List files by regex - several answers (1)

• Download

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: 2008-09-27

Credits: Alan Williams

List files by extension - empty directory (1)

• Download

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The empty directory is examined by the List_files_by_extension service. Since no files end in ".png", an empty list is output.

Created: 2008-09-27

Credits: Alan Williams

List files by extension - no answer (1)

• Download

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_extension service. Since no files end in ".fred", an empty list is output.

Created: 2008-09-27

Credits: Alan Williams

List files by extension - single answer (1)

• Download

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_extension service and the file path to the one file ending in ".bin" is output.

Created: 2008-09-27

Credits: Alan Williams

List files by extension - several answers (1)

• Download

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_extension service and the file paths to the three files ending in ".png" are output.

Created: 2008-09-27

Credits: Alan Williams

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

• Download

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: 2008-09-27

Credits: Alan Williams

Get web page from URL - just url (1)

• Download

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: 2008-09-27

Credits: Alan Williams

Get image URLs from HTTP document (1)

• Download

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: 2008-09-27

Credits: Alan Williams

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

• Download

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

Created: 2008-09-27

Credits: Alan Williams

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

• Download

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

Created: 2008-09-27

Credits: Alan Williams

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

• Download

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: 2008-09-27

Credits: Alan Williams

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

• Download

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: 2008-09-27

Credits: Alan Williams

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

• Download

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

Created: 2008-09-27

Credits: Alan Williams

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

• Download

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

Created: 2008-09-27

Credits: Alan Williams

Fail if true - non true value (1)

• Download

The fail if true service executes without an exception if given a value that is not true e.g. 'fred'.

Created: 2008-09-27

Credits: Alan Williams