Workflows

Ajusting galaxy paramenters using sextractor (5)

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This workflow creates configuration files for sextractor, it runs sextractor using this configuration files, it adds sextractor results to the input votable and adds new calculated columns. This task requires a votable as input, a template, a vocabulary and the specification of the column names that contain some required files (configuration files, image files, ...). These files must be accesible from taverna. Sextractor is called by an bash script as 'sex'. Every row in the votable cotains ...

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: Julian Garrido

Attributions: Create configuration files from a template and a votable Run sextractor using a votable Create votable from sextractor results Add columns to a votable resulting from executing sextractor.

Create votable from sextractor results (2)

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The workflow creates a votable from the results provided by sextractor (votables). It returns this table and an aditional table that is joined to the input table. It requires a votable that contains a column with the file name resulting from running sextractor and such files accesible from taverna. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/).

Created: 2012-07-26 | Last updated: 2012-08-21

Credits: Julian Garrido

Run sextractor using a votable (2)

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It runs sextractor and adjust the paramenters specified. This workflow has a dependency on the stil library (http://www.star.bris.ac.uk/~mbt/stil/). Sextractor is called by an bash script as 'sex'. Sextractor is called for every row in the votable. Columns where the configuration file and the image file name are defined must be especified. These files should be accesibles from taverna. ExperimentFolder provides the root folder for the experiment. If the configuration files contain refer...

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: Julian Garrido

13C NMR spectra prediction (2)

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This workflow can be used to predict the 13C NMR spectra of a molecule. The generation of the structure of the molecule is done using the IUPAC to Structure node that uses OPSIN to convert the name of the molecule to a structure. Alternativelly, one can read the structure from a file. The spectra prediction is based on the NMRShiftDB implementation and the data used is also from NMRShiftDB. The atom topological environments were represented as Atom Signatures and used to calculate the checmia...

Created: 2012-07-26 | Last updated: 2012-08-10

Credits: Ldpf

Create configuration files from a template... (1)

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This workflow uses astrotaverna artifacts. It creates files by using a template whose keys are replaced by data from a votable. A configuration file is created for every row in the votable. The keys must appear also in the vocabulary file and match column names in the votable. A column in the votable must contain the name of the result configuration file.

Created: 2012-07-26 | Last updated: 2012-09-04

Credits: Julian Garrido

Check the content of the Registry for mism... (1)

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This workflow check for tables which are registered in the HELIO registry but not available in the UOC and for tables which are in the UOC but which are not registred.

Created: 2012-07-25

Credits: Anja Le Blanc

Check registry for wrongly registed and un... (2)

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HELIO registry contains a list of tables available in the HEC. The HEC contains a table with available talbes itself. This workflow shows the differences between these two lists.

Created: 2012-07-24 | Last updated: 2012-07-24

Credits: Anja Le Blanc

RTTS Mapper (1)

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Generates RTTS counts file from SAM file. Output consists of three columns: counts at given position;chromosome;position(0 based). Workflow removes untemplated nucleotides from 5' ends of the reads. Authors: Jeppe Vinther, Lukasz Kielpinski Workflow published by lukaszkielpinski on Galaxy Jun 26, 2012 imported to myExperiment Jul 17, 2012 during demonstration of Galaxy-myExperiment integration (specifically generating SVG and showing steps of more complex workflow).

Created: 2012-07-17 | Last updated: 2012-07-17

Transform 'Stitch Gene blocks' FASTA block... (1)

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Converts FASTA blocks to a FASTA file. Workflow published by galaxyproject on Galaxy Jun 27, 2012 imported to myExperiment Jul16, 2012 during demonstration of Galaxy-myExperiment integration  https://main.g2.bx.psu.edu/u/galaxyproject/w/transform-stitch-gene-blocks-fasta-blocks-to-standardized-fasta-file

Created: 2012-07-16 | Last updated: 2012-07-16

Basic Illumina Reads Quality (Functional G... (1)

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From the RNA-Seq analysis tutorial during the Functional Genomics Workshop 2012 https://caps.osu.edu/pfg-workshop Workflow published by mejia-guerra on Galaxy Jun 22, 2012 imported to myExperiment Jul16, 2012 during demonstration of Galaxy-myExperiment integration

Created: 2012-07-16 | Last updated: 2012-07-16

Basic RNA-Seq Analysis - Differential Expr... (1)

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From the RNA-Seq analysis tutorial during the Functional Genomics Workshop 2012 https://caps.osu.edu/pfg-workshop Workflow published by mejia-guerra on Galaxy Jun 22, 2012 imported to myExperiment Jul16, 2012 during demonstration of Galaxy-myExperiment integration  

Created: 2012-07-16 | Last updated: 2012-07-16

AnnotationTimes (1)

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This very simple workflow was used in the analysis of the metadata produced by the human annotation phase of the SALAMI (Strucural Analysis of Large Amounts of Music Inforamtion) project.  The input data is the metadata available from http://ddmal.music.mcgill.ca/salami/annotations It produces a histogram of song durations and scatterplot of combined annotation time verus song duration. The fields are   SONG_ID                   Un...

Created: 2012-07-16 | Last updated: 2012-07-16

Example of how to use Sesame service and V... (1)

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This workflow needs as input a list of names of galaxies. Then it queries Sesame services to get the coordinates of this galaxies, and finally with this coordinates queries a Virtual Observatory Services (a cone service).

Created: 2012-07-14

Gene to Pathways (Vistrails) (1)

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This is a Vistrails workflow that returns the pathways of a given gene ID. In doing so, it uses two kegg services.

Created: 2012-07-10

Credits: Khalid Belhajjame

Gene to Pathways (1)

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This is a Taverna workflow that given a gene ID fetches the corespondondings pathways. To do so, the workflow make use of two KEGG web services.

Created: 2012-07-09 | Last updated: 2012-07-10

Credits: Khalid Belhajjame

List Concept Sets (3)

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Pupose: The workflow returns a list of all Concept Set IDs currently available in the database. The Concept Sets have an hierarchical structure that can be inferred by referring to the parent Concept Set ID.

Created: 2012-07-06 | Last updated: 2014-07-14

Credits: Kristina Hettne Marco Roos Reinout van Schouwen Martijn Schuemie BioSemantics

Get concept information (5)

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The workflow takes a (list of) concept ID(s) as input and returns the profile, ID, definition and name of the concept.

Created: 2012-07-06 | Last updated: 2014-07-14

Credits: Kristina Hettne Reinout van Schouwen Marco Roos Martijn Schuemie BioSemantics

Get Concept IDs (5)

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Purpose: The workflow retrieves the concepts within a concept set. The Web service/workflow currently returns no values (bug).

Created: 2012-07-06 | Last updated: 2014-07-14

Credits: Kristina Hettne Reinout van Schouwen Martijn Schuemie Marco Roos BioSemantics

Task Data Pattern (BeanShell) (1)

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This is a sample implementation of "Task Data" pattern intoduced workflowPatterns.com It defines a variable inside a Beanshell and uses the passed value through the processors input. Details: http://www.workflowpatterns.com/patterns/data/visibility/wdp1.php

Created: 2012-07-06

Get all applications available on the HPS (1)

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This workflow requests all available applications on the HPS which do not require authentication to run. No inputs. Outputs contain all information to execute the application on the HPS such as the ID of the application and the names of all parameters.

Created: 2012-07-03

Credits: Anja Le Blanc