| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/srst2/srst2/0.2.0+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/srst2/srst2/0.2.0+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/srst2/srst2/0.2.0+galaxy0 |
| srst2 |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| samtools | 0.1.18 | package |
| srst2 | 0.2.0 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input|paired_input1: ERR024070_1_reduced_forward_reads.fastqsanger.gz input|paired_input2: ERR024070_2_reduced_reverse_reads.fastqsanger.gz input|merge_paired: False input|read_type: q input|selector: paired use_mlst_db|mlst_db: Escherichia_coli1R.fasta use_mlst_db|mlst_definitions: profiles_csv use_mlst_db|mlst_delimiter: _ use_mlst_db|mlst_max_mismatch: 10 use_mlst_db|min_depth: 5 use_mlst_db|min_edge_depth: 2 use_mlst_db|selector: yes use_gene_db|gene_db: ARGannotR.fasta use_gene_db|no_gene_details: True use_gene_db|gene_max_mismatch: 10 use_gene_db|min_coverage: 90 use_gene_db|max_divergence: 10 use_gene_db|selector: yes output_files_selector: ['log', 'save_scores', 'report_new_consensus', 'report_all_consensus'] prob_err: 0.01 max_unaligned_overlap: 10 mapq: 1 baseq: 20 |
name: value name: value name: value name: value |
ERR024070_1_reduced_forward_reads.fastqsanger.gz ERR024070_2_reduced_reverse_reads.fastqsanger.gz Escherichia_coli1R.fasta profiles_csv ARGannotR.fasta value |
| Test-2 |
input|paired_input1: ERR024070_1_reduced_forward_reads.fastqsanger.gz input|paired_input2: ERR024070_2_reduced_reverse_reads.fastqsanger.gz input|merge_paired: False input|read_type: q input|selector: paired use_mlst_db|selector: no use_gene_db|selector: no output_files_selector: ['log', 'save_scores', 'report_new_consensus', 'report_all_consensus'] prob_err: 0.01 max_unaligned_overlap: 10 mapq: 1 baseq: 20 |
name: value name: value name: value |
ERR024070_1_reduced_forward_reads.fastqsanger.gz ERR024070_2_reduced_reverse_reads.fastqsanger.gz value |