0: View complete virus identification
Version 1

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Run on usegalaxy.eu

Work-in-progress

Non-functional workflow to get a global view of possibilities for plant virus classification.

SEEK ID: https://workflowhub.eu/workflows/100?version=1

Inputs

ID	Name	Description	Type
single_paired	single_paired	runtime parameter for tool fastp	n/a
single_paired	single_paired	runtime parameter for tool fastp	n/a
single_paired	single_paired	runtime parameter for tool Kraken2	n/a
query	query	runtime parameter for tool NCBI BLAST+ blastn	n/a
query	query	runtime parameter for tool NCBI BLAST+ tblastx	n/a
input_hmm_conditional	input_hmm_conditional	runtime parameter for tool hmmscan	n/a
seqfile	seqfile	runtime parameter for tool hmmscan	n/a
library	library	runtime parameter for tool Shovill	n/a
fastq_input	fastq_input	runtime parameter for tool Map with minimap2	n/a
excludebed	excludebed	runtime parameter for tool BAM filter	n/a
includebed	includebed	runtime parameter for tool BAM filter	n/a
excludebed	excludebed	runtime parameter for tool BAM filter	n/a
includebed	includebed	runtime parameter for tool BAM filter	n/a

Steps

ID	Name	Description
0	fastp	toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
1	FLASH merge read	toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4
2	Kraken2	toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy0
3	FASTA Merge Files and Filter Unique Sequences	toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0
4	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2
5	NCBI BLAST+ blastn	toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0
6	NCBI BLAST+ tblastx	toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/2.10.1+galaxy0
7	hmmscan	toolshed.g2.bx.psu.edu/repos/iuc/hmmer_hmmscan/hmmer_hmmscan/3.3+galaxy1
8	Shovill	toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0
9	Convert Kraken	toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/Kraken2Tax/1.2
10	Map with minimap2	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2
11	Krona pie chart	toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0
12	BAM filter: keep unmapped reads	toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9
13	BAMfilter : keep mapped reads	toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9
14	SamToFastq	toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2
15	Shovill	toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0
16	NCBI BLAST+ blastn	toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0

Outputs

ID	Name	Description	Type
out1	out1	n/a	input
out2	out2	n/a	input
report_html	report_html	n/a	html
merged_paired_reads	merged_paired_reads	n/a	input
unmerged_paired_reads_f	unmerged_paired_reads_f	n/a	input
unmerged_paired_reads_r	unmerged_paired_reads_r	n/a	input
hist	hist	n/a	tabular
log	log	n/a	txt
output	output	n/a	tabular
output	output	n/a	fasta
alignment_output	alignment_output	n/a	bam
output1	output1	n/a	tabular
output1	output1	n/a	tabular
output	output	n/a	txt
tblout	tblout	n/a	txt
domtblout	domtblout	n/a	txt
pfamtblout	pfamtblout	n/a	txt
shovill_std_log	shovill_std_log	n/a	txt
contigs	contigs	n/a	fasta
contigs_graph	contigs_graph	n/a	txt
out_file	out_file	n/a	taxonomy
alignment_output	alignment_output	n/a	bam
output	output	n/a	html
outfile	outfile	n/a	bam
outfile	outfile	n/a	bam
fq_single	fq_single	n/a	fastqsanger
interleaved_fastq	interleaved_fastq	n/a	fastqsanger
fq1	fq1	n/a	fastqsanger
fq2	fq2	n/a	fastqsanger
fq_u	fq_u	n/a	fastqsanger
shovill_std_log	shovill_std_log	n/a	txt
contigs	contigs	n/a	fasta
contigs_graph	contigs_graph	n/a	txt
output1	output1	n/a	tabular

Creators and Submitter

Creators

Not specified

Submitter

johan Rollin

License

Apache Software License 2.0

Activity

Views: 68 Downloads: 4

Created: 4th Feb 2021 at 09:05

Last used: 16th Apr 2021 at 06:49

Version History

Version 1 Created 4th Feb 2021 at 09:05 by johan Rollin

No revision comments

0: View complete virus identification Version 1