All content

View Download

Example input for EBI_InterproScan_NewServices

Created: 2014-04-09 16:15:28

Credits: Christian

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

Comments: 0 | Viewed: 21 times | Downloaded: 15 times

This File has no tags!

Photohawk PAE tiff/png/jpeg (5)

• Download

SCAPE QA Object Component. Compares tiff/png/jpeg images using Photohawk PAE.

Created: 2014-04-09 | Last updated: 2014-10-30

Photohawk MSE tiff/png/jpeg (3)

• Download

SCAPE QA Object Component. Compares tiff/png/jpeg images using Photohawk MSE.

Created: 2014-04-09 | Last updated: 2014-10-30

Photohawk MAE tiff/png/jpeg (3)

• Download

SCAPE QA Object Component. Compares tiff/png/jpeg images using Photohawk MAE.

Created: 2014-04-09 | Last updated: 2014-10-30

Photohawk equal tiff/png/jpeg (2)

• Download

SCAPE QA Object Component. Compares tiff/png/jpeg images using Photohawk equal.

Created: 2014-04-09 | Last updated: 2014-09-07

Photohawk AE tiff/png/jpeg (3)

• Download

SCAPE QA Object Component. Compares tiff/png/jpeg images using Photohawk AE.

Created: 2014-04-09 | Last updated: 2014-10-30

Tool for detecting changes in web pages an... (1)

• Download

SCAPE QA Object Component

Created: 2014-04-07

Credits: Zeynep Pehlivan

Toy workflow (1)

• Download

This is just a toy workflow

Created: 2014-04-04

Credits: Khalid Belhajjame

Toy workflow (1)

• Download

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

Credits: Khalid Belhajjame

ONB Web Archive Fits Characterisation usin... (1)

• Download

Wrapper workflow for workflow 3933 to produce a test series, the nested workflow is executed with a set of "num_files_per_invokation" parameters.

Created: 2014-04-04

Compute and correct GC bias in NGS data (1)

• Download

Galaxy workflow based on deepTools which will compute and correct GC bias in your NGS data. For more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.

Created: 2014-04-03

Credits: Björn Grüning

Remove "chr" from the beginning of genomic... (1)

• Download

Created: 2014-04-03

Credits: Björn Grüning

Add "chr" to the first column of a 6 colum... (1)

• Download

Created: 2014-04-03

Credits: Björn Grüning

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

• Download

Created: 2014-04-03

Credits: Björn Grüning

Heatmap of read coverages (1)

• Download

Created: 2014-04-03

Credits: Björn Grüning

Clustered heatmap of signals around the TSSs (1)

• Download

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

View Download

GBIF

Created: 2014-04-03 13:11:49

1 item in this pack

Comments: 0 | Viewed: 44 times | Downloaded: 20 times

Unix tool service using string replacement (1)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

Perform multiple iterations of services in order to show pipelining

Created: 2014-04-03

Credits: Alex Nenadic

Numerically adding two values. (1)

• Download

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)

• Download

A fun example workflow showing user-interaction and service looping

Created: 2014-04-03

Credits: Alex Nenadic

Hello World (1)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

This workflow demonstrates how nested workflows can be conditionally invoked

Created: 2014-04-03

Credits: Alex Nenadic

Example for external tools with zip and unzip (1)

• Download

This workflow only works on a Unix machine. This workflow takes a fixed URL from which a text file is downloaded (output as Original_file). That file is zipped (output as Zipped_File) and then unzipped again (output as Unzipped_File). The orginal file and the unzipped version are then diff'd/

Created: 2014-04-03

Credits: Alex Nenadic

EBI_InterproScan_NewServices (2)

• Download

This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text and xml. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.

Created: 2014-04-03 | Last updated: 2014-04-09

Credits: Alex Nenadic

Demonstration of configurable iteration (2)

• Download

This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2014-04-03 | Last updated: 2014-07-09

Credits: Alex Nenadic

View Download

Taverna 2.5 Bioinformatics Starter Pack

Created: 2014-04-02 12:44:47 | Last updated: 2017-01-09 13:08:53

18 items in this pack

Comments: 0 | Viewed: 86 times | Downloaded: 38 times

View Download

Taverna 2.5 Biodiversity Starter Pack

Created: 2014-04-02 12:40:42 | Last updated: 2017-01-09 13:09:17

14 items in this pack

Comments: 0 | Viewed: 85 times | Downloaded: 29 times

Photohawk SSIM tiff/png/jpeg (4)

• Download

SCAPE QA Object Component. Compares tiff/png/jpeg images using Photohawk SSIM.

Created: 2014-04-01 | Last updated: 2014-10-30

calculateFieldline by SINP (5)

• Download

Workflow for Taverna based on the IMPEx-FP7 method calculateFieldLine. This method can be used to return the field lines (calculated by SINP PMM), which start in given points inside the planetary magnetosphere and in different time moments for each point, and the magnetic field along these lines.

Created: 2014-03-31 | Last updated: 2014-05-19

calculateDataPointValue by SINP (3)

• Download

Workflow for Taverna based on the IMPEx-FP7 method calculateDataPointValue. This method can be used to return the magnetic field (calculated by SINP PMM) in given points inside the planetary magnetosphere and in different time moments for each point.

Created: 2014-03-31 | Last updated: 2014-05-19

getMostRelevantRun by FMI (3)

• Download

Workflow for Taverna based on the IMPEx-FP7 method getMostRelevantRun. This method is intended to help users to find those simulation runs in SMDB's tree.xml file whose input parameters best match the given solar wind conditions. For each simulation run in the tree.xml file the method computes a 'difference index'. This 'difference index' is a sum of individual difference indices (one for each solar wind parameter defined in the input parameter set).

Created: 2014-03-31 | Last updated: 2014-05-19

getFileUrl by LATMOS (5)

• Download

Workflow for Taverna based on the IMPEx-FP7 method getFileURL. This method fetches precomputed data, i.e. already calculated values along a given spacecraft trajectory.

Created: 2014-03-31 | Last updated: 2014-05-19

getFieldline by LATMOS (3)

• Download

Workflow for Taverna based on the IMPEx-FP7 method getFieldLine. This method computes field lines or stream lines inside the simulation box. The user will provide a set of 3D position coordinates which act as starting points for the field/stream line tracing. The tracing may be performed forwards, backwards or both. The method will return an URL to a VOTable file which contains the field/stream lines as a set of 3D position coordinates and the requested physical quantities at these points.

Created: 2014-03-31 | Last updated: 2014-05-20

getFieldline by FMI (3)

• Download

Workflow for Taverna based on the IMPEx-FP7 method getFieldLine. This method computes field lines or stream lines inside the simulation box. The user will provide a set of 3D position coordinates which act as starting points for the field/stream line tracing. The tracing may be performed forwards, backwards or both. The method will return an URL to a VOTable file which contains the field/stream lines as a set of 3D position coordinates and the requested physical quantities at these points.

Created: 2014-03-31 | Last updated: 2014-05-19

getDataPointValue_Spacecraft by LATMOS (4)

• Download

Workflow for Taverna based on the IMPEx-FP7 method getDataPointValue_Spacecraft. This method is used to compute values of various physical quantities (e.g. density, magnetic field strength etc.) along the path of a given spacecraft.

Created: 2014-03-31 | Last updated: 2014-05-19

getDataPointValue_Spacecraft by FMI (3)

• Download

Workflow for Taverna based on the IMPEx-FP7 method getDataPointValue_Spacecraft. This method is used to compute values of various physical quantities (e.g. density, magnetic field strength etc.) along the path of a given spacecraft.

Created: 2014-03-31 | Last updated: 2014-05-20