Metavisitor: Spades test in Use Case 2-2

Created: 2016-10-10 15:20:50 Last updated: 2016-10-10 15:59:52

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

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Workflow Components

Inputs (9)

Name	Description
Input Dataset Collection
Protein Blast database
library	runtime parameter for tool Bowtie2
input	runtime parameter for tool Concatenate multiple datasets
input	runtime parameter for tool Filter sequences by length
db_opts	runtime parameter for tool NCBI BLAST+ blastx
query	runtime parameter for tool NCBI BLAST+ blastx
blast	runtime parameter for tool Parse blast output and compile hits
sequences	runtime parameter for tool Parse blast output and compile hits

Steps (8)

Name	Tool	Description
Input dataset collection	None
Input dataset	None
Bowtie2	toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2
Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2
spades	toolshed.g2.bx.psu.edu/repos/nml/spades/spades/1.4
Filter sequences by length	toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1
NCBI BLAST+ blastx	toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.06
Parse blast output and compile hits	toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3

Outputs (19)

Name	Type
output_unaligned_reads_l	fastqsanger
output_aligned_reads_l	fastqsanger
output_aligned_reads_r	fastqsanger
output_unaligned_reads_r	fastqsanger
output	bam
output_sam	sam
mapping_stats	txt
out_file1	input
out_contigs	fasta
out_contig_stats	tabular
out_scaffolds	fasta
out_scaffold_stats	tabular
out_log	txt
output	fasta
output1	tabular
tabularOutput	tabular
fastaOutput	fasta
al_sequences	fasta
un_sequences	fasta