| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/2.55+galaxy4 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/2.55+galaxy3 |
| toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/2.55+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/2.55+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/2.55+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/2.53+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/2.4+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/2.4+galaxy0 |
| stacks2_populations |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| stacks | 2.55 | package |
| python | 3.7 | package |
| findutils | 4.6.0 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
options_usage|input_aln: list collection options_usage|input_type: stacks popmap: denovo_map/popmap_cstacks.tsv batch_size: 9999 add_log: True |
name: value name: value name: value name: value name: value name: value |
gstacks/catalog.calls.vcf gstacks/catalog.fa.gz denovo_map/popmap_cstacks.tsv value |
| Test-2 |
options_usage|input_aln: list collection options_usage|input_type: stacks add_log: True |
name: value name: value name: value name: value name: value name: value |
gstacks/catalog.calls.vcf gstacks/catalog.fa.gz value |
| Test-3 |
options_usage|input_aln: list collection options_usage|input_type: stacks popmap: denovo_map/popmap_cstacks.tsv fstats_conditional|fstats: yes populations_output|fasta_loci: True populations_output|fasta_samples: True populations_output|vcf: True populations_output|genepop: True populations_output|structure: True populations_output|radpainter: True populations_output|plink: True populations_output|hzar: True populations_output|phylip: True populations_output|phylip_var: True populations_output|treemix: True populations_output|fasta_samples_raw: True populations_output|gtf: True advanced_options|log_fst_comp: True add_log: True |
name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value |
gstacks/catalog.calls.vcf gstacks/catalog.fa.gz denovo_map/popmap_cstacks.tsv value |
| Test-4 |
options_usage|input_vcf: gstacks/catalog.calls.vcf options_usage|input_type: vcf popmap: denovo_map/popmap_cstacks.tsv add_log: True |
name: value name: value name: value name: value name: value name: value |
gstacks/catalog.calls.vcf denovo_map/popmap_cstacks.tsv value |
| Test-5 |
options_usage|input_aln: list collection options_usage|input_type: stacks popmap: denovo_map/popmap_cstacks.tsv options_filtering|minperc: 0.1 options_filtering|minpop: 2 options_filtering|min_samples_overall: 0.01 options_filtering|filter_haplotype_wise: True options_filtering|min_maf: 0.01 options_filtering|min_mac: 1 options_filtering|max_obs_het: 0.8 options_filtering|blacklist: populations/blacklist.tsv add_log: True |
name: value name: value name: value name: value name: value name: value |
gstacks/catalog.calls.vcf gstacks/catalog.fa.gz denovo_map/popmap_cstacks.tsv populations/blacklist.tsv value |
| Test-6 |
options_usage|input_aln: list collection options_usage|input_type: stacks popmap: denovo_map/popmap_cstacks.tsv options_filtering|minperc: 0.1 options_filtering|minpop: 2 options_filtering|min_samples_overall: 0.01 options_filtering|min_maf: 0.01 options_filtering|min_mac: 1 options_filtering|max_obs_het: 0.8 options_filtering|filter_single_snp: --write-single-snp options_filtering|blacklist: populations/blacklist.tsv add_log: True |
name: value name: value name: value name: value name: value name: value |
gstacks/catalog.calls.vcf gstacks/catalog.fa.gz denovo_map/popmap_cstacks.tsv populations/blacklist.tsv value |
| Test-7 |
options_usage|input_aln: list collection options_usage|input_type: stacks popmap: denovo_map/popmap_cstacks.tsv merge_phase|enzyme: ecoRI merge_phase|merge_sites: True merge_phase|merge_prune_lim: 0.9 locus_stats|hwe: True add_log: True |
name: value name: value name: value name: value name: value name: value |
gstacks/catalog.calls.vcf gstacks/catalog.fa.gz denovo_map/popmap_cstacks.tsv value |
| Test-8 |
options_usage|input_aln: list collection options_usage|input_type: stacks popmap: denovo_map/popmap_cstacks_genotypes.tsv fstats_conditional|fst_correction: True fstats_conditional|p_value_cutoff: 0.01 fstats_conditional|fstats: yes kernel_smoothing|options_kernel|sigma: 150001 kernel_smoothing|options_kernel|kernel: -k kernel_smoothing|bootstrap_resampling_mode|bootstrap: --bootstrap kernel_smoothing|bootstrap_reps: 23 add_log: True |
name: value name: value name: value name: value name: value name: value name: value name: value name: value |
refmap/catalog.calls.vcf refmap/catalog.fa.gz denovo_map/popmap_cstacks_genotypes.tsv value |
| Test-9 |
options_usage|input_aln: list collection options_usage|input_type: stacks popmap: denovo_map/popmap_cstacks.tsv fstats_conditional|fstats: no kernel_smoothing|options_kernel|sigma: 150001 kernel_smoothing|options_kernel|kernel: --smooth-fstats kernel_smoothing|bootstrap_resampling_mode|bootstrap: --bootstrap kernel_smoothing|bootstrap_reps: 23 add_log: True |
name: value name: value name: value name: value name: value name: value name: value name: value name: value |
refmap/catalog.calls.vcf refmap/catalog.fa.gz denovo_map/popmap_cstacks.tsv value |
| Test-10 |
options_usage|input_aln: list collection options_usage|input_type: stacks popmap: denovo_map/popmap_cstacks.tsv add_log: True |
name: value name: value name: value name: value name: value name: value |
gstacks/catalog.calls.vcf gstacks/catalog.fa.gz denovo_map/popmap_cstacks.tsv value |
| Test-11 |
options_usage|input_aln: list collection options_usage|input_type: stacks popmap: denovo_map/popmap_cstacks_genotypes.tsv genetic_map_options|map_type: CP genetic_map_options|map_format: joinmap add_log: True |
name: value name: value name: value name: value name: value name: value name: value |
gstacks/catalog.calls.vcf gstacks/catalog.fa.gz denovo_map/popmap_cstacks_genotypes.tsv value |