| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/ragtag/ragtag/2.1.0+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/ragtag/ragtag/2.1.0+galaxy0 (this tool) |
| ragtag |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| ragtag | 2.1.0 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
mode_conditional|reference: genome.fna mode_conditional|query: contigs.fna mode_conditional|advanced_options|e: reference_headers_skip.txt mode_conditional|advanced_options|j: query_headers_skip.txt mode_conditional|advanced_options|f: 1000 mode_conditional|advanced_options|remove_small: False mode_conditional|advanced_options|q: 10 mode_conditional|advanced_options|d: 100000 mode_conditional|advanced_options|mapping_conditional|mm2_params: asm5 mode_conditional|advanced_options|mapping_conditional|mapping_option: minimap2 mode_conditional|advanced_options|b: 5000 mode_conditional|advanced_options|missasembly_break: --inter mode_conditional|advanced_options|gff: annotation.gff mode_conditional|output_correct: ['fasta', 'agp', 'paf', 'log'] mode_conditional|mode_option: correct |
name: value name: value name: value name: value |
genome.fna contigs.fna reference_headers_skip.txt query_headers_skip.txt annotation.gff value |
| Test-2 |
mode_conditional|reference: genome.fna mode_conditional|query: contigs.fna mode_conditional|advanced_options|f: 1000 mode_conditional|advanced_options|remove_small: True mode_conditional|advanced_options|q: 10 mode_conditional|advanced_options|d: 100000 mode_conditional|advanced_options|mapping_conditional|mapping_option: nucmer mode_conditional|advanced_options|b: 5000 mode_conditional|advanced_options|missasembly_break: --inter mode_conditional|output_correct: ['fasta', 'agp'] mode_conditional|mode_option: correct |
name: value name: value |
genome.fna contigs.fna value |
| Test-3 |
mode_conditional|reference: genome.fna mode_conditional|query: contigs.fna mode_conditional|advanced_options|f: 1000 mode_conditional|advanced_options|remove_small: True mode_conditional|advanced_options|q: 10 mode_conditional|advanced_options|d: 100000 mode_conditional|advanced_options|i: 0.2 mode_conditional|advanced_options|a: 0 mode_conditional|advanced_options|s: 0 mode_conditional|output_scaffold: ['fasta', 'agp', 'paf', 'confidence', 'log', 'stats'] mode_conditional|mode_option: scaffold |
name: value name: value name: value name: value name: value name: value |
genome.fna contigs.fna value |
| Test-4 |
mode_conditional|reference: genome.fna mode_conditional|query: contigs.fna mode_conditional|advanced_options|s: 50000 mode_conditional|advanced_options|i: 0.05 mode_conditional|output_patch: ['final_fasta', 'final_agp', 'assembly_file', 'split_assembly', 'split_description', 'target_gaps', 'agp_renamed', 'fasta_renamed', 'log'] mode_conditional|mode_option: patch |
name: value name: value name: value name: value name: value name: value name: value name: value name: value |
genome.fna contigs.fna value |
| Test-5 |
mode_conditional|assembly_fasta: correct_fasta_01.fasta mode_conditional|scaffold_files: ['correct_agp_01.agp', 'correct_agp_02.agp'] mode_conditional|merging_options|l: 100000 mode_conditional|merging_options|e: 0 mode_conditional|merging_options|function_merging: min mode_conditional|mode_option: merge |
name: value name: value |
correct_fasta_01.fasta correct_agp_01.agp correct_agp_02.agp value |