0: View complete virus identification
Version 1

Work-in-progress

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

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
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Views: 68   Downloads: 4

Created: 4th Feb 2021 at 09:05

Last used: 16th Apr 2021 at 06:49

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Version History

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

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