Workflows

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

getDataPointValue by LATMOS (5)

• Download

Workflow for Taverna based on the IMPEx-FP7 method getDataPointValue. This is a generic method which can be used to return parameters for 0D, 1D, 2D, or 3D.

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

getDataPointValue by FMI (3)

• Download

Workflow for Taverna based on the IMPEx-FP7 method getDataPointValue. This method is used to compute values of various physical quantitites (e.g. density, magnetic field strengths etc.) for a given simulation run at a user given set of 3D points.

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

calculateCubeMercury by SINP (3)

• Download

Workflow for Taverna based on the IMPEx-FP7 method calculateCubeMercury. This method returns the magnetic field, calculated by SINP PMM, in grid points of a cube with chosen boundaries inside the Hermean magnetosphere with chosen sampling.

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

MergePeptides (1)

• Download

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

Credits: hindlem

An iframe test (1)

• Download

But this works

Created: 2014-03-28

Credits: Alan Williams

calculateDataPointValueMercury by SINP (6)

• Download

Workflow for Taverna based on the IMPEx-FP7 method calculateDataPointValueMercury. This method can be used to return the magnetic field (calculated by SINP PMM) in given points inside the Hermean magnetosphere.

Created: 2014-03-28 | Last updated: 2014-05-19

Credits: Manuel Scherf

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: 2014-03-28 | Last updated: 2014-05-20

calculateCube by SINP (3)

• Download

Workflow for Taverna based on the IMPEx-FP7 method calculateCube. This calculates a 3DCube based on the paraboloid model of SINP around Earth (see http://smdc.sinp.msu.ru/index.py?nav=paraboloid/index).

Created: 2014-03-28 | Last updated: 2014-05-19

Finding wrong links in Linked Open Data wi... (1)

• Download

This simple workflow shows how to detect wrong links in Linked Open Data. It uses operators from the Linked Open Data and the Anomaly Detection extensions. The process first reads a list of links from the EventMedia endpoint, linking to DBpedia, then creates feature vectors for each of those links. Finally, an outlier detection operator is employed to find suspicious links.

Created: 2014-03-14

XPath From VOTable (1)

• Download

A XPath From text version for VOTables. This is useful to extract certain information from the header of the VOTables but it could work for any XPath.

Created: 2014-03-12

Credits: David PS Anja Le Blanc

Attributions: Extracting data from VOTable format by using XPath query

test_workflow (2)

• Download

test_upload

Created: 2014-03-10 | Last updated: 2014-03-10

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: 2014-03-06

ARC2WARC Hadoop Job (1)

• Download

Just a wrapper workflow for a Hadoop job converting ARC to WARC files.

Created: 2014-03-06

Credits: Sven

NGS : Tuto SNP detection workflow single end (1)

• Download

Generate pileup, Unify Genotypers and create a VCF file from FastQ files of two individuals

Created: 2014-03-05 | Last updated: 2014-06-10

Credits: Ylebras

NGS RAD : Population Genomics on RAD data ... (1)

• Download

Analyse clean population fastQ files (coming from Stacks : Process Radtag tool for example) without a reference genome and population information

Created: 2014-03-05

NGS RAD : Population Genomics on RAD data ... (1)

• Download

Analyse clean population SAM files (coming from alignment of FastQ from Stacks : Process Radtag tool for example) with a reference genome and population information

Created: 2014-03-05 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Group and filter mapped reads (1)

• Download

Filter and group reads from a mapping Bam file

Created: 2014-03-05 | Last updated: 2014-06-10

Credits: Ylebras

Tuto Galaxy 2013 : GenOuest, from Fasta to... (1)

• Download

Create a tree from a multifastafile using ClustalW, PhylipDNAdist, PhylipNeighbor, PhylipDrawtree and Treevector, for interactive visualization in Phyloviz or static on pdf or svg format. Then, using the same multifasta file, handling sequences file, use blast on a reference genome and filter results to have sequences with more than 90% identity.

Created: 2014-03-05 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Tuto SNP detection workflow single end (1)

• Download

Generate pileup, Unify Genotypers and create a VCF file from FastQ files of two individuals

Created: 2014-03-04 | Last updated: 2014-06-10

Credits: Ylebras

Transcritomics : eQTL after data extractio... (1)

• Download

Format raw files from Feature extraction output (Agilent array matrix file) to have individual in columns and genes in rows

Created: 2014-03-04 | Last updated: 2014-06-10

Credits: Ylebras

ToMaR HDFS Input Directory Processing (2)

• Download

This workflow allows processing an HDFS input directory using ToMaR. The "hdfs_working_dir" input port is the HDFS input directory which containes the data to be processed by ToMaR. The "toolspec" input port contains the toolspec XML describing operations that can be used (see "operation" input port). The "operation" input port defines the operation to be used in the current ToMaR job execution (see "toolspec" input port, an operation port used here must be defined in the tool specificatio...

Created: 2014-03-04 | Last updated: 2014-03-11

Credits: Sven

NGS : RNAseq workflow part 1 from Tophat t... (1)

• Download

Remove duplicates from Tophat BAM output files and filter

Created: 2014-03-04 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Mini assembly from FastQ files using... (1)

• Download

Assemble FastQ reads with minia

Created: 2014-02-28 | Last updated: 2014-06-10

Credits: Ylebras

pubmed abstracts from pathways (1)

• Download

Extraction of the abstracts from pubmed pubblications related to the pathways involving the input genes

Created: 2014-02-28

Credits: Massimo La Rosa Antonino Fiannaca

Attributions: NCBI Gi to Kegg Pathway Descriptions Pathway to Pubmed

NGS : Filter contamination in raw reads by ID (1)

• Download

Filter FastQ sequences by ID

Created: 2014-02-28 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Bowtie2 using built-in genome to dep... (1)

• Download

Reads mapping using a built-in genome from your history, then generate pileup, base coverage, depth of coverage and summary statistics

Created: 2014-02-28 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Bowtie2 with a genome in fasta forma... (1)

• Download

Reads mapping using a reference genome in fasta format from your history, then generate pileup, base coverage, depth of coverage and summary statistics

Created: 2014-02-28 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Coverage determination and visualiza... (1)

• Download

From a BAM file and a reference genome fasta file, calculate the depth of coverage and generate pileup, interval, Base coverage as Summary statistics

Created: 2014-02-28 | Last updated: 2014-06-10

Credits: Ylebras

NGS : flanking SNP regions (1)

• Download

Flank SNP regions using interval format file and a fasta reference file

Created: 2014-02-28 | Last updated: 2014-06-10

Credits: Ylebras

Population genomics : From Blast xml forma... (1)

• Download

Parse Blast XML results to obtain species specifics sequences

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

NGS : RNA-seq differential expression anal... (1)

• Download

Analyse paired-end RNA-seq reads of 2 different individuals with FastQC, Tophat2, Cufflinks and Cuffdiff using a reference annotation in gtf format

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Filtrer fastq reads with N (1)

• Download

Filter FastQ file and delete sequences with N

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

Population genomics : Structure and CLUMPP (1)

• Download

Population genomics analysis using Structure and Clumpp to cluster data

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

NGS : FastQ Quality check and FastQ manipu... (1)

• Download

Taking FastQ reads, apply FastQ groomer on sequences and generate Quality reports (FastQC, Summary statistics, boxplots) before and after filter

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

Invocation of instrument location service (1)

• Download

Invocation of the Instrument Location Service (ILS) located in Paris Observatory.

Created: 2014-02-27

Credits: Eoincar

Helio Feature Catalogue Invocation (1)

• Download

Simple invocation of the helio feature catalogue using the service located at Paris Observatory

Created: 2014-02-27

Credits: Eoincar

Instrument Capability Service Invocation w... (1)

• Download

This workflow is an invocation ofthe Instrument Capability Service using the HELIO plugin built by Kevin Benson

Created: 2014-02-27

Invocation of instrument capability service (1)

• Download

Simple invocation of the instrument capability service (ICS). Also shows what tables and table fields are available for searching.

Created: 2014-02-27

Credits: Eoincar

Tuto Galaxy 2013 : CPB2012 - BasicProtocol... (1)

• Download

Workflow used when applying the CPB2012 Basic Protocol 1 tutorial from Galaxy team. It permits to filter Exons with the most SNP density.

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Pair reads assembly with Velvet Work... (1)

• Download

Paired-end reads assembly after fastQ groomer using a Migale (France INRA core facility https://migale.jouy.inra.fr/) modified version of Velvet tool suite descriptors

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

Tuto Galaxy 2013 : CPB2012 - BasicProtocol... (1)

• Download

Workflow used when applying the CPB2012 Basic Protocol 3 tutorial from Galaxy team. It calls peaks for ChIP-seq data using MACS14.

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

Imagemagick convert - image2tiff - compres... (1)

• Download

Converts images supported by imagemagick to tiff using imagemagick convert with the provided compression

Created: 2014-02-14

Credits: Markus Plangg

Converts any ImageMagick supported image f... (1)

• Download

SCAPE Migration Component

Created: 2014-02-12

Credits: Markus Plangg

Curves Exploration (1)

• Download

Exploration of curves of cubes that contain galaxy observations

Created: 2014-02-12

Credits: Julian Garrido