| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.11.0+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.11.0+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.11.0+galaxy0 |
| staramr_search |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| staramr | 0.11.0 | package |
| mlst | 2.23.0 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
hide_db_build: true genomes: 16S-rc_gyrA-rc_beta-lactam.fsa staramr_db_select: staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 pointfinder_organism: salmonella advanced|pid_threshold: 98.0 advanced|percent_length_overlap_resfinder: 60.0 advanced|percent_length_overlap_pointfinder: 95.0 advanced|percent_length_overlap_plasmidfinder: 60.0 advanced|genome_size_lower_bound: 4000000 advanced|genome_size_upper_bound: 6000000 advanced|minimum_N50_value: 10000 advanced|minimum_contig_length: 300 advanced|unacceptable_number_contigs: 1000 advanced|report_all_blast: False advanced|exclude_negatives: False advanced|exclude_resistance_phenotypes: False advanced|mlst_scheme: auto advanced|exclude_genes|exclude_genes_condition: default advanced|plasmidfinder_type: include_all output_files|output_selection: ['mlst_table', 'summary_table', 'detailed_summary_table', 'resfinder_table', 'plasmidfinder_table', 'pointfinder_table', 'settings_output', 'excel_output'] |
name: value name: value name: value name: value name: value |
16S-rc_gyrA-rc_beta-lactam.fsa value |
| Test-2 |
hide_db_build: true genomes: 16S-rc_gyrA-rc_beta-lactam.fsa staramr_db_select: staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 pointfinder_organism: escherichia_coli advanced|pid_threshold: 98.0 advanced|percent_length_overlap_resfinder: 60.0 advanced|percent_length_overlap_pointfinder: 95.0 advanced|percent_length_overlap_plasmidfinder: 60.0 advanced|genome_size_lower_bound: 4000000 advanced|genome_size_upper_bound: 6000000 advanced|minimum_N50_value: 10000 advanced|minimum_contig_length: 300 advanced|unacceptable_number_contigs: 1000 advanced|report_all_blast: False advanced|exclude_negatives: False advanced|exclude_resistance_phenotypes: False advanced|mlst_scheme: auto advanced|exclude_genes|exclude_genes_condition: default advanced|plasmidfinder_type: include_all output_files|output_selection: ['mlst_table', 'summary_table', 'detailed_summary_table', 'resfinder_table', 'plasmidfinder_table', 'pointfinder_table', 'settings_output', 'excel_output'] |
name: value name: value name: value name: value name: value |
16S-rc_gyrA-rc_beta-lactam.fsa value |
| Test-3 |
hide_db_build: true genomes: 16S-rc_gyrA-rc_beta-lactam.fsa staramr_db_select: staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 pointfinder_organism: disabled advanced|pid_threshold: 98.0 advanced|percent_length_overlap_resfinder: 60.0 advanced|percent_length_overlap_pointfinder: 95.0 advanced|percent_length_overlap_plasmidfinder: 60.0 advanced|genome_size_lower_bound: 4000000 advanced|genome_size_upper_bound: 6000000 advanced|minimum_N50_value: 10000 advanced|minimum_contig_length: 300 advanced|unacceptable_number_contigs: 1000 advanced|report_all_blast: False advanced|exclude_negatives: False advanced|exclude_resistance_phenotypes: False advanced|mlst_scheme: auto advanced|exclude_genes|exclude_genes_condition: default advanced|plasmidfinder_type: include_all output_files|output_selection: ['mlst_table', 'summary_table', 'detailed_summary_table', 'resfinder_table', 'plasmidfinder_table', 'settings_output', 'excel_output'] |
name: value name: value |
16S-rc_gyrA-rc_beta-lactam.fsa value |
| Test-4 |
hide_db_build: true genomes: 16S-rc_gyrA-rc_beta-lactam.fsa staramr_db_select: staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 pointfinder_organism: disabled advanced|pid_threshold: 98.0 advanced|percent_length_overlap_resfinder: 60.0 advanced|percent_length_overlap_pointfinder: 95.0 advanced|percent_length_overlap_plasmidfinder: 60.0 advanced|genome_size_lower_bound: 4000000 advanced|genome_size_upper_bound: 6000000 advanced|minimum_N50_value: 10000 advanced|minimum_contig_length: 300 advanced|unacceptable_number_contigs: 1000 advanced|report_all_blast: False advanced|exclude_negatives: False advanced|exclude_resistance_phenotypes: False advanced|mlst_scheme: listeria_2 advanced|exclude_genes|exclude_genes_condition: default advanced|plasmidfinder_type: include_all output_files|output_selection: ['mlst_table', 'summary_table', 'detailed_summary_table', 'resfinder_table', 'plasmidfinder_table', 'settings_output', 'excel_output'] |
name: value |
16S-rc_gyrA-rc_beta-lactam.fsa value |
| Test-5 |
hide_db_build: true genomes: 16S-rc_gyrA-rc_beta-lactam.fsa staramr_db_select: staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 pointfinder_organism: disabled advanced|pid_threshold: 99.8 advanced|percent_length_overlap_resfinder: 60.0 advanced|percent_length_overlap_pointfinder: 95.0 advanced|percent_length_overlap_plasmidfinder: 60.0 advanced|genome_size_lower_bound: 4000000 advanced|genome_size_upper_bound: 6000000 advanced|minimum_N50_value: 10000 advanced|minimum_contig_length: 300 advanced|unacceptable_number_contigs: 1000 advanced|report_all_blast: False advanced|exclude_negatives: False advanced|exclude_resistance_phenotypes: False advanced|mlst_scheme: auto advanced|exclude_genes|exclude_genes_condition: default advanced|plasmidfinder_type: include_all output_files|output_selection: ['mlst_table', 'summary_table', 'detailed_summary_table', 'resfinder_table', 'plasmidfinder_table', 'settings_output', 'excel_output'] |
name: value |
16S-rc_gyrA-rc_beta-lactam.fsa value |
| Test-6 |
hide_db_build: true genomes: 16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa staramr_db_select: staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 pointfinder_organism: disabled advanced|pid_threshold: 99.8 advanced|percent_length_overlap_resfinder: 60.0 advanced|percent_length_overlap_pointfinder: 95.0 advanced|percent_length_overlap_plasmidfinder: 60.0 advanced|genome_size_lower_bound: 4000000 advanced|genome_size_upper_bound: 6000000 advanced|minimum_N50_value: 10000 advanced|minimum_contig_length: 300 advanced|unacceptable_number_contigs: 1000 advanced|report_all_blast: False advanced|exclude_negatives: False advanced|exclude_resistance_phenotypes: False advanced|mlst_scheme: auto advanced|exclude_genes|exclude_genes_condition: default advanced|plasmidfinder_type: include_all output_files|output_selection: ['mlst_table', 'summary_table', 'detailed_summary_table', 'resfinder_table', 'plasmidfinder_table', 'settings_output', 'excel_output'] |
name: value |
16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa value |
| Test-7 |
hide_db_build: true genomes: test-aminoglycoside.fsa staramr_db_select: staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 pointfinder_organism: disabled advanced|pid_threshold: 98.0 advanced|percent_length_overlap_resfinder: 60.0 advanced|percent_length_overlap_pointfinder: 95.0 advanced|percent_length_overlap_plasmidfinder: 60.0 advanced|genome_size_lower_bound: 4000000 advanced|genome_size_upper_bound: 6000000 advanced|minimum_N50_value: 10000 advanced|minimum_contig_length: 300 advanced|unacceptable_number_contigs: 1000 advanced|report_all_blast: False advanced|exclude_negatives: False advanced|exclude_resistance_phenotypes: False advanced|mlst_scheme: auto advanced|exclude_genes|exclude_genes_condition: default advanced|plasmidfinder_type: include_all output_files|output_selection: ['mlst_table', 'summary_table', 'detailed_summary_table', 'resfinder_table', 'plasmidfinder_table', 'settings_output', 'excel_output'] |
name: value |
test-aminoglycoside.fsa value |
| Test-8 |
hide_db_build: true genomes: test-aminoglycoside.fsa staramr_db_select: staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 pointfinder_organism: disabled advanced|pid_threshold: 98.0 advanced|percent_length_overlap_resfinder: 60.0 advanced|percent_length_overlap_pointfinder: 95.0 advanced|percent_length_overlap_plasmidfinder: 60.0 advanced|genome_size_lower_bound: 4000000 advanced|genome_size_upper_bound: 6000000 advanced|minimum_N50_value: 10000 advanced|minimum_contig_length: 300 advanced|unacceptable_number_contigs: 1000 advanced|report_all_blast: False advanced|exclude_negatives: False advanced|exclude_resistance_phenotypes: False advanced|mlst_scheme: auto advanced|exclude_genes|exclude_genes_condition: none advanced|plasmidfinder_type: include_all output_files|output_selection: ['mlst_table', 'summary_table', 'detailed_summary_table', 'resfinder_table', 'plasmidfinder_table', 'settings_output', 'excel_output'] |
name: value |
test-aminoglycoside.fsa value |
| Test-9 |
hide_db_build: true genomes: test-aminoglycoside.fsa staramr_db_select: staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 pointfinder_organism: disabled advanced|pid_threshold: 98.0 advanced|percent_length_overlap_resfinder: 60.0 advanced|percent_length_overlap_pointfinder: 95.0 advanced|percent_length_overlap_plasmidfinder: 60.0 advanced|genome_size_lower_bound: 4000000 advanced|genome_size_upper_bound: 6000000 advanced|minimum_N50_value: 10000 advanced|minimum_contig_length: 300 advanced|unacceptable_number_contigs: 1000 advanced|report_all_blast: False advanced|exclude_negatives: False advanced|exclude_resistance_phenotypes: False advanced|mlst_scheme: auto advanced|exclude_genes|exclude_genes_file: genes_to_exclude.tsv advanced|exclude_genes|exclude_genes_condition: custom advanced|plasmidfinder_type: include_all output_files|output_selection: ['mlst_table', 'summary_table', 'detailed_summary_table', 'resfinder_table', 'plasmidfinder_table', 'settings_output', 'excel_output'] |
name: value |
test-aminoglycoside.fsa genes_to_exclude.tsv value |
| Test-10 |
hide_db_build: true genomes: test-aminoglycoside.fsa staramr_db_select: staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 pointfinder_organism: disabled advanced|pid_threshold: 98.0 advanced|percent_length_overlap_resfinder: 60.0 advanced|percent_length_overlap_pointfinder: 95.0 advanced|percent_length_overlap_plasmidfinder: 60.0 advanced|genome_size_lower_bound: 1 advanced|genome_size_upper_bound: 10 advanced|minimum_N50_value: 10000 advanced|minimum_contig_length: 300 advanced|unacceptable_number_contigs: 1000 advanced|report_all_blast: False advanced|exclude_negatives: False advanced|exclude_resistance_phenotypes: False advanced|mlst_scheme: auto advanced|exclude_genes|exclude_genes_condition: default advanced|plasmidfinder_type: include_all output_files|output_selection: ['mlst_table', 'summary_table', 'detailed_summary_table', 'resfinder_table', 'plasmidfinder_table', 'settings_output', 'excel_output'] |
name: value |
test-aminoglycoside.fsa value |