| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/drep_dereplicate/drep_dereplicate/3.3.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/drep_dereplicate/drep_dereplicate/3.2.2+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/drep_dereplicate/drep_dereplicate/2.5.4.0 |
| drep_dereplicate |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| drep | 3.2.2 | package |
| checkm-genome | 1.1.3 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
genomes: ['Enterococcus_casseliflavus_EC20.fasta', 'Enterococcus_faecalis_T2.fna', 'Enterococcus_faecalis_TX0104.fa'] filter|length: 50000 filter|completeness: 75 filter|contamination: 100 quality|checkM_method: taxonomy_wf quality|checkm_group_size: 2000 quality|source: checkm comp_clust|steps|MASH_sketch: 1000 comp_clust|steps|P_ani: 0.9 comp_clust|steps|multiround_primary_clustering: False comp_clust|steps|primary_chunksize: 5000 comp_clust|steps|clustering|n_PRESET: normal comp_clust|steps|clustering|coverage_method: larger comp_clust|steps|clustering|S_algorithm: ANImf comp_clust|steps|S_ani: 0.99 comp_clust|steps|cov_thresh: 0.1 comp_clust|steps|select: default comp_clust|clusterAlg: average comp_clust|run_tertiary_clustering: False scoring|completeness_weight: 1 scoring|contamination_weight: 5 scoring|strain_heterogeneity_weight: 1 scoring|N50_weight: .5 scoring|size_weight: 0 scoring|centrality_weight: 1 warning|warn_dist: 0.25 warning|warn_sim: 0.98 warning|warn_aln: 0.25 select_outputs: ['log', 'warnings', 'Primary_clustering_dendrogram', 'Clustering_scatterplots', 'Cluster_scoring', 'Winning_genomes', 'Widb'] |
name: value |
Enterococcus_casseliflavus_EC20.fasta Enterococcus_faecalis_T2.fna Enterococcus_faecalis_TX0104.fa value |
| Test-2 |
genomes: ['001', '002', '003'] filter|length: 50000 filter|completeness: 75 filter|contamination: 100 quality|checkM_method: taxonomy_wf quality|checkm_group_size: 2000 quality|source: checkm comp_clust|steps|MASH_sketch: 1000 comp_clust|steps|P_ani: 0.9 comp_clust|steps|multiround_primary_clustering: False comp_clust|steps|primary_chunksize: 5000 comp_clust|steps|clustering|n_PRESET: normal comp_clust|steps|clustering|coverage_method: larger comp_clust|steps|clustering|S_algorithm: ANImf comp_clust|steps|S_ani: 0.99 comp_clust|steps|cov_thresh: 0.1 comp_clust|steps|select: default comp_clust|clusterAlg: average comp_clust|run_tertiary_clustering: False scoring|completeness_weight: 1 scoring|contamination_weight: 5 scoring|strain_heterogeneity_weight: 1 scoring|N50_weight: .5 scoring|size_weight: 0 scoring|centrality_weight: 1 warning|warn_dist: 0.25 warning|warn_sim: 0.98 warning|warn_aln: 0.25 select_outputs: ['log', 'warnings', 'Primary_clustering_dendrogram', 'Clustering_scatterplots', 'Cluster_scoring', 'Winning_genomes', 'Widb'] |
name: value |
001 002 003 value |