0: View complete virus identification Version 1
Download RO Crate
Run on usegalaxy.euNon-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 | |
| out2 | out2 | n/a | |
| report_html | report_html | n/a | |
| merged_paired_reads | merged_paired_reads | n/a | |
| unmerged_paired_reads_f | unmerged_paired_reads_f | n/a | |
| unmerged_paired_reads_r | unmerged_paired_reads_r | n/a | |
| hist | hist | n/a | |
| log | log | n/a | |
| output | output | n/a | |
| output | output | n/a | |
| alignment_output | alignment_output | n/a | |
| output1 | output1 | n/a | |
| output1 | output1 | n/a | |
| output | output | n/a | |
| tblout | tblout | n/a | |
| domtblout | domtblout | n/a | |
| pfamtblout | pfamtblout | n/a | |
| shovill_std_log | shovill_std_log | n/a | |
| contigs | contigs | n/a | |
| contigs_graph | contigs_graph | n/a | |
| out_file | out_file | n/a | |
| alignment_output | alignment_output | n/a | |
| output | output | n/a | |
| outfile | outfile | n/a | |
| outfile | outfile | n/a | |
| fq_single | fq_single | n/a | |
| interleaved_fastq | interleaved_fastq | n/a | |
| fq1 | fq1 | n/a | |
| fq2 | fq2 | n/a | |
| fq_u | fq_u | n/a | |
| shovill_std_log | shovill_std_log | n/a | |
| contigs | contigs | n/a | |
| contigs_graph | contigs_graph | n/a | |
| output1 | output1 | n/a |
Creators and SubmitterViews: 364 Downloads: 20
Created: 4th Feb 2021 at 09:05
Last used: 22nd Jan 2022 at 15:58
AttributionsNone
Version History
Version 1 (earliest) Created 4th Feb 2021 at 09:05 by johan Rollin
Added/updated 1 files
Open
master531b52e
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Teams: Integrated and Urban Plant Pathology Laboratory
Organizations: Liege university
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, Genomics Coordination Center, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC, Probabilistic graphical models, GenX, Snakemake-Workflows, ODA, IPK BIT, CO2MICS Lab, FAME, CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus, Quadram Institute Bioscience - Bioinformatics, HecatombDevelopment, Institute of Human Genetics, Testing RO Crates, Test Team, Applied Computational Biology at IEG/HMGU, INFRAFRONTIER workflows, OME, TransBioNet, OpenEBench, Galaxycompchem, Bioinformatics and Biostatistics (BIO2 ) Core
Web page: Not specified
Les recherches et enseignements développés par le Laboratoire de Phytopathologie Intégrée et Urbaine visent à améliorer la protection des plantes contre les maladies provoquées par les agents pathogènes et à développer de nouveaux modes de production agricole en milieu urbain. Le laboratoire contribue ainsi à répondre aux défis écologiques, environnementaux, climatiques et sociétaux de l’agriculture de demain.
Space: Independent Teams
Public web page: https://www.gembloux.ulg.ac.be/phytopathologie/
