vir-representative

Created: 2016-08-09 13:55:48 Last updated: 2016-08-09 13:57:55

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Retrieve from NCBI and reduce redundancy in the viral database.

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Inputs (27)

Name	Description
input	runtime parameter for tool Compute sequence length
input	runtime parameter for tool FASTA-to-Tabular
files	runtime parameter for tool Multi-Join
first_file	runtime parameter for tool Multi-Join
files	runtime parameter for tool Multi-Join
first_file	runtime parameter for tool Multi-Join
files	runtime parameter for tool Multi-Join
first_file	runtime parameter for tool Multi-Join
inputs	runtime parameter for tool Concatenate datasets
infile	runtime parameter for tool Sort
infile	runtime parameter for tool Sort
input	runtime parameter for tool Tabular-to-FASTA
input	runtime parameter for tool Tabular-to-FASTA
input	runtime parameter for tool UCLUST
input	runtime parameter for tool Filter sequences by length
input	runtime parameter for tool Filter sequences by length
input	runtime parameter for tool UCLUST
input	runtime parameter for tool FASTA Width
input1	runtime parameter for tool PSI-CD-HIT
inputs	runtime parameter for tool Concatenate datasets
input	runtime parameter for tool FASTA Width
input	runtime parameter for tool FASTA Width
input	runtime parameter for tool FASTA Width
input	runtime parameter for tool Compute sequence length
input	runtime parameter for tool FASTA-to-Tabular
input	runtime parameter for tool Compute sequence length
input	runtime parameter for tool FASTA-to-Tabular

Steps (27)

Name	Tool	Description
Retrieve FASTA from NCBI	testtoolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.3
Retrieve FASTA from NCBI	testtoolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.3
Compute sequence length	toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.0
FASTA-to-Tabular	toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0
Multi-Join	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.0.0
Multi-Join	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.0.0
Multi-Join	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.0.0
Concatenate datasets	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0
Sort	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.0.0
Sort	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.0.0
Tabular-to-FASTA	toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0
Tabular-to-FASTA	toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0
Retrieve FASTA from NCBI	testtoolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.3
UCLUST	usearch
Filter sequences by length	toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1
Filter sequences by length	toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1
UCLUST	usearch
FASTA Width	toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.0
PSI-CD-HIT	testtoolshed.g2.bx.psu.edu/repos/pegoraro/psicdhit/psi-cd-hit/0.1.0
Concatenate datasets	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0
FASTA Width	toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.0
FASTA Width	toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.0
FASTA Width	toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.0
Compute sequence length	toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.0
FASTA-to-Tabular	toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0
Compute sequence length	toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.0
FASTA-to-Tabular	toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0

Outputs (34)

Name	Type
outfilename	fasta
logfile	txt
outfilename	fasta
logfile	txt
output	tabular
output	tabular
outfile	input
outfile	input
outfile	input
out_file1	input
outfile	input
outfile	input
output	fasta
output	fasta
outfilename	fasta
logfile	txt
uc	text
centroids	fasta
output	fasta
output	fasta
uc	text
centroids	fasta
output	input
output1	fasta
outputclstr	txt
outputout	txt
out_file1	input
output	input
output	input
output	input
output	tabular
output	tabular
output	tabular
output	tabular

Information Workflow Type

Galaxy

Information Uploader

Juliana Pegoraro

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Juliana Pegoraro

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Information Statistics

546 viewings

417 downloads

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Citations (0)

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Version History

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vir-representative

Created by Juliana Pegoraro on Tuesday 09 August 2016 13:55:47 (UTC)

Last edited by Juliana Pegoraro on Tuesday 09 August 2016 13:57:54 (UTC)

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