Workflow Entry: Compare two genomes for similarity

Created at: 17/03/10 @ 11:01:09 Last updated: 17/03/10 @ 11:05:00

Version 4 (latest) (of 4)

Version created on: 17/03/10 @ 11:01:09 by: Gregg Iceton | Revision comments Expand

Last edited on: 17/03/10 @ 11:05:01 by: Gregg Iceton

Title: Compare two genomes for similarity

Type: Taverna 2

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Description

This workflow takes the file path to two genome nucleotide files in fasta format and requests a minimum similarity required from the user. The genomes are aligned according to the M-GCAT algorithm (http://alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html) and the genome similarity parsed out of the resultant log file. Output is either 0 (genome similarity less than required similarity) or 1 (genome similarity equal to or greater than the required similarity).

NB - The file paths to the sequence files MUST be provided, not the sequences themselves!

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http://www.myexperiment.org/workflows/1123/download?version=4
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Workflow Components

Authors (0)

Titles (0)

Descriptions (0)

Inputs (2)

Name	Description
Sequence1
Sequence2

Processors (24)

Name	Type	Description
runMGCAT	localworker
MGCAT_Path	stringconstant
Working_Dir	stringconstant
Read_Text_File	localworker
Split_string_into_string_list_by_regular_expression	localworker
Regex1	stringconstant
Filter_List_of_Strings_by_regex	localworker
Regex2	stringconstant
Regex3	stringconstant
Write_Text_File	localworker
Concatenate_strings	localworker
Group	stringconstant
INI_File	stringconstant
Read_Text_File_2	localworker
Split_string_into_string_list_by_regular_expression_2	localworker
Regex1_2	stringconstant
Filter_list_of_strings_extracting_match_to_a_regex	localworker
Group1	stringconstant
regex2	stringconstant
Thresholder	beanshell
Ask	localworker
Message	stringconstant
Title	stringconstant
INI_Path	stringconstant

Beanshells (1)

Name	Description	Inputs	Outputs
Thresholder		seqSim reqSim	cont

Outputs (1)

Name	Description
continue

Datalinks (26)

Source	Sink
MGCAT_Path:value	runMGCAT:command
Working_Dir:value	runMGCAT:workingdir
INI_File:value	runMGCAT:args
INI_Path:value	Read_Text_File:fileurl
Read_Text_File:filecontents	Split_string_into_string_list_by_regular_expression:string
Regex1:value	Split_string_into_string_list_by_regular_expression:regex
Split_string_into_string_list_by_regular_expression:split	Filter_List_of_Strings_by_regex:stringlist
Regex2:value	Filter_List_of_Strings_by_regex:regex1
Regex3:value	Filter_List_of_Strings_by_regex:regex2
Sequence2	Filter_List_of_Strings_by_regex:file2
Group:value	Filter_List_of_Strings_by_regex:group
Sequence1	Filter_List_of_Strings_by_regex:file
Concatenate_strings:output	Write_Text_File:filecontents
INI_Path:value	Write_Text_File:outputFile
Filter_List_of_Strings_by_regex:filteredlist	Concatenate_strings:stringlist
Working_Dir:value	Read_Text_File_2:fileurl
Read_Text_File_2:filecontents	Split_string_into_string_list_by_regular_expression_2:string
Regex1_2:value	Split_string_into_string_list_by_regular_expression_2:regex
Split_string_into_string_list_by_regular_expression_2:split	Filter_list_of_strings_extracting_match_to_a_regex:stringlist
Group1:value	Filter_list_of_strings_extracting_match_to_a_regex:group
regex2:value	Filter_list_of_strings_extracting_match_to_a_regex:regex
Filter_list_of_strings_extracting_match_to_a_regex:filteredlist	Thresholder:seqSim
Ask:answer	Thresholder:reqSim
Message:value	Ask:message
Title:value	Ask:title
Thresholder:cont	continue

Coordinations (7)

Controller	Target
Write_Text_File	runMGCAT
runMGCAT	Read_Text_File_2
Write_Text_File	Working_Dir
Concatenate_strings	Write_Text_File
Write_Text_File	INI_File
Write_Text_File	MGCAT_Path
Filter_List_of_Strings_by_regex	Concatenate_strings