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Workflow Designer Manual

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Created by Yuliya Algaer, last modified on Aug 21, 2013

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About the Workflow Designer
Introduction
Launching Workflow Designer
Workflow Designer Window Components
Workflow Elements and Connections
Managing Parameters
UGENE Components and Workflow Designer
Task View, Notifications and Log View
Actions Menu
Toolbar
Context Menus
Application Settings
How to Create and Run Workflow
Manipulating Element
Adding Element
Copying Element
Pasting Element
Cutting Element
Deleting Element
Selecting All Elements on Scene
Manipulating Workflow
Creating New Workflow
Loading Workflow
Saving Workflow
Exporting Workflow as Image
Validating Workflow
Running Workflow
Dashboard
Dashboard Window Components
Using Dashboard
Stopping and Pausing Workflow
Changing Appearance
Custom Elements with Scripts
Functions Supported for Multiple Alignment Data
Functions Supported for Sequence Data
Functions Supported for Set of Annotations Data
Functions Supported for Files
Common Function
Custom Elements with Command Line Tools
Creating Element
Editing Element
Adding Existent Element
Removing Element
Using Script to Set Parameter Value
Running Workflow from the Command Line
Running Workflow in Debugging Mode
Creating Breakpoints
Manipulating Breakpoints
Workflow File Format
Header
Body
Elements
Dataflow
Metainformation
Workflow Elements
Data Readers
File List Element
Read Alignment Element
Read Annotations Element
Read Assembly Element
Read from DAS Element
Read from Remote Database Element
Read Plain Text Element
Read Sequence Element
Read Variations Element
Data Writers
Write Alignment Element
Write Annotations Element
Write Assembly Element
Write FASTA Element
Write Plain Text Element
Write Sequence Element
Write Variations Element
Data Flow
Filter Element
Grouper Element
Multiplexer Element
Sequence Marker Element
Basic Analysis
Amino Translations Element
Annotate with DAS Element
Annotate with UQL Element
CD-Search Element
Collocation Search Element
Export PHRED Qualities Element
Fetch Sequences by ID From Annotation Element
Filter Annotation by Name Element
Filter Annotations by Qualifier
Find Pattern Element
Find Repeats Element
Gene-by-gene approach report
Get Sequences by Annotations Element
Import PHRED Qualities Element
Local BLAST Search Element
Local BLAST+ Search Element
Merge Annotations Element
ORF Marker Element
Remote BLAST Element
Remove Duplicates in BAM Files Element
Smith-Waterman Search Element
Data Converters
Convert bedGraph Files to bigWig Element
Convert Text to Sequence Element
File Format Conversion Element
Reverse Complement Element
Split Assembly into Sequences Element
DNA Assembly
Align reads with BWA-MEM
Assembly Sequences with CAP3
Extract Consensus from Assembly
HMMER2 Tools
HMM Build Element
HMM Search Element
Read HMM Profile Element
Write HMM Profile Element
HMMER3 Tools
HMM3 Build Element
HMM3 Search Element
Read HMM3 Profile
Write HMM3 Profile
Multiple Sequence Alignment
Align Profile to Profile with MUSCLE Element
Align with ClustalO Element
Align with ClustalW Element
Align with Kalign Element
Align with MAFFT Element
Align with MUSCLE Element
Align with T-Coffee Element
Extract Consensus from Alignment
Join Sequences into Alignment Element
Split Alignment into Sequences Element
NGS: Basic
CASAVA FASTQ Filter Element
FASTQ Quality Trimmer Element
Filter BAM/SAM Files Element
Genome Coverage Element
Merge BAM Files Element
Slopbed Element
Sort BAM Files Element
NGS: ChiP-Seq Analysis
Annotate Peaks with peak2gene Element
Build Conservation Plot Element
Collect Motifs with SeqPos Element
Conduct GO Element
Create CEAS Report Element
Find Peaks with MACS Element
NGS: RNA-Seq Analysis
Assembly Transcripts with Cufflinks Element
Extract Transcript Sequences with gffread Element
Find Splice Junction with TopHat Element
Merge Assemblies with Cuffmerge Element
Test for Diff. Expression with Cuffdiff Element
NGS: Variant Calling
Call Variants with SAMtools Element
Create VCF consensus
SNP Annotation
Annotate variations with SNPToolbox Element
Detect Transcription Factors with rSNP-Tools Element
Determine SNP effect on TATA-boxes Element
ProtStability1D Element
ProtStability3D Element
SNP Chip Tools Element
SNP Effect on PDB sites Element
Write SNP Report Element
Transcription Factor
Build Frequency Matrix Element
Build SITECON Model Element
Build Weight Matrix Element
Convert Frequency Matrix Element
Read Frequency Matrix Element
Read SITECON Model Element
Read Weight Matrix Element
Search for TFBS with SITECON Element
Search for TFBS with Weight Matrix Element
Write Frequency Matrix Element
Write SITECON Model Element
Write Weight Matrix Element
Utils
DNA Statistics Element
Generate DNA Element
Custom Elements With Script
CASAVA FASTQ Filter Script Element
Dump Sequence Info Element
FASTQ Trimmer Element
LinkData Fetch Element
Quality Filter Element
Workflow Samples
Alignment
Align sequences with MUSCLE
Conversions
Convert seq/qual pair to Fastq
Convert alignments to ClustalW
Convert UQL schema results to alignment
Convert sequence to Genbank
Custom elements
CASAVA FASTQ Filter
FASTQ Trimmer
Dump sequence info
LinkData fetch
Quality filter
Data Marking
Marking Sequences by Annotation Number
Marking Sequences by Length
Data Merging
Find Substrings at Sequences
Merge Sequences and Shift Corresponding Annotations
Search for TFBS
HMMER
Build HMM from alignment and test it
Search sequences with profile HMM
NGS
Call Variants with SAMtools
ChIP-seq Analysis with Cistrome Tools
Extract Consensus
Extract transcript sequences
RNA-seq Analysis with Tuxedo Tools
Scenarios
Filter sequence that match a pattern
Find patterns
Gene-by-gene approach for characterization of genomes
Merge sequences and annotations
Transcriptomics
Search for transcription factor binding sites (TFBS) in genomic sequences

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