Workflows

Heatmap of read coverages (single BAM file) (1)

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Created: 2014-04-03

Credits: Björn Grüning

Heatmap of read coverages (1)

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Created: 2014-04-03

Credits: Björn Grüning

Clustered heatmap of signals around the TSSs (1)

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Galaxy workflow based on deepTools which creates a clustered heatmap of signals around the TSS. One bigwig file is needed as input with the signal and an annotation file with your TSS regions. The output will be a heatmap. You can create such a bigwig file with the bamCorrelate toolFor more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.

Created: 2014-04-03 | Last updated: 2014-04-03

Credits: Björn Grüning

Unix tool service using string replacement (1)

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The tool service outputs a message that greets using the names specified on Greet's input ports.

Created: 2014-04-03

Credits: Alex Nenadic

Spreadsheet Import Example (1)

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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date. The source data is from http://data.gov.uk/

Created: 2014-04-03

Credits: Alex Nenadic

Simple Python example (1)

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This workflow generates a random number within the range 0 to 100. The generation is done by a python script. The workflow assumes that python is in the path.

Created: 2014-04-03

Credits: Alex Nenadic

Secure Web service call example (1)

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This is an example of a workflow that contains a call to a secure Web service that runs behind HTTPS and requires user to authenticate. The first thing you can expect to see is a pop up dialog asking if you trust the Web service to be invoked over HTTPS. You can use testuser/testpasswd as username and password for authentication when running the workflow. To see where the security is being configured, right-click the service in the diagram and select "Configure security" from the menu. You m...

Created: 2014-04-03

Credits: Alex Nenadic

Secure REST service call example (1)

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This is an example of a workflow that contains a call to a secure REST service that requires user to authenticate with HTTP Basic Authentication. You can use testuser/testpasswd as username and password for authentication when running the workflow.

Created: 2014-04-03

Credits: Alex Nenadic

Render gene via BioGPS (1)

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This workflow uses the REST API of BioGPS to list the plugins and then allow the user to select which plugin to use to display the input gene id

Created: 2014-04-03

Credits: Alex Nenadic

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2014-04-03

Credits: Alex Nenadic

Numerically adding two values. (1)

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This workflow relies on a Unix system. It wraps the "bc" command line calculator. It downloads the calculation script from a URL.

Created: 2014-04-03

Credits: Alex Nenadic

Multiple choice quiz (1)

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A fun example workflow showing user-interaction and service looping

Created: 2014-04-03

Credits: Alex Nenadic

Hello World (1)

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One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".

Created: 2014-04-03

Credits: Alex Nenadic

Hello Anyone (1)

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An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".

Created: 2014-04-03

Credits: Alex Nenadic

GBSeq test (1)

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2014-04-03

Credits: Alex Nenadic

Fetch today's xkcd comic (1)

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Use the local services and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2014-04-03

Credits: Alex Nenadic

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2014-04-03

Credits: Alex Nenadic

Example workflow for REST and XPath activi... (1)

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This workflow fetches weather forecast for the user-specified location. First of all it uses the provided location name to obtain a WOEID ("Where On Earth ID") of that location, then uses that unique identifier to fetch the weather forecast from Yahoo server. Multiple results may be obtained in case there is no unique translation of the location to a WOEID. REST activity is used to perform HTTP requests and fetch data from remote servers; XPath activity is then used to parse the XML data a...

Created: 2014-04-03

Credits: Alex Nenadic

Example of explicit looping (1)

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This workflow demonstrates how a nested workflow can be called an explicit number of times. Note that the loop iterator does not need to be used in the logic of the loop contents. It can be used as a sentinel (see the conditional workflow)

Created: 2014-04-03

Credits: Alex Nenadic

Example of conditional invocation (1)

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This workflow demonstrates how nested workflows can be conditionally invoked

Created: 2014-04-03

Credits: Alex Nenadic