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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Activity
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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