Metavisitor: Workflow for small RNA profiling of contigs

Created: 2016-10-10 07:43:44 Last updated: 2016-10-10 08:22:56

Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence data

Mississippi Galaxy server

Not currently available.

Inputs (10)

Name	Description
Input Dataset Collection of fastq reads
de novo assembled Oases contigs
input	runtime parameter for tool Clip adapter
input	runtime parameter for tool Filter sequences by length
input	runtime parameter for tool Concatenate multiple datasets
input	runtime parameter for tool Regex Find And Replace
input	runtime parameter for tool sRbowtie
refGenomeSource	runtime parameter for tool sRbowtie
gff	runtime parameter for tool Generate readmap and histograms from alignment files
refGenomeSource	runtime parameter for tool Generate readmap and histograms from alignment files

Steps (8)

Name	Tool	Description
Input dataset collection	None
Input dataset	None
Clip adapter	toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6
Filter sequences by length	toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1
Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2
Regex Find And Replace	toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0
sRbowtie	toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2
Generate readmap and histograms from alignment files	toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.1.5

Outputs (12)

Name	Type
output	fasta
output	fasta
out_file1	input
out_file1	input
output	tabular
aligned	fasta
unaligned	fasta
readmap_dataframe	tabular
size_distribution_dataframe	tabular
readmap_PDF	pdf
size_PDF	pdf
combi_PDF	pdf