Repository revision
2:38942a7e3801

Repository 'stacks2_populations'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations

Stacks2: populations tool metadata
Miscellaneous
Calculate population-level summary statistics
stacks2_populations
toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/2.4+galaxy1
2.4+galaxy1
process_radtags -h |& grep process_radtags | head -n 1 | cut -d" " -f 2
True
Version lineage of this tool (guids ordered most recent to oldest)
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 (this tool)
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 2.4 package
Functional tests
name inputs outputs required files
Test-1 options_usage|input_type: stacks
popmap: denovo_map/popmap_cstacks.tsv
add_log: True
batch_size: 9999
options_usage|input_aln: list collection
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
gstacks/catalog.calls.vcf
gstacks/catalog.fa.gz
denovo_map/popmap_cstacks.tsv
name
Test-2 options_usage|input_type: stacks
add_log: True
options_usage|input_aln: list collection
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
gstacks/catalog.calls.vcf
gstacks/catalog.fa.gz
name
Test-3 populations_output|fasta_samples_raw: True
options_usage|input_type: stacks
populations_output|fasta_samples: True
populations_output|plink: True
add_log: True
popmap: denovo_map/popmap_cstacks.tsv
populations_output|structure: True
populations_output|hzar: True
fstats_conditional|fstats: yes
populations_output|phylip_var: True
populations_output|treemix: True
populations_output|radpainter: True
populations_output|phylip: True
populations_output|genepop: True
options_usage|input_aln: list collection
populations_output|fasta_loci: True
advanced_options|log_fst_comp: True
populations_output|vcf: True
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
gstacks/catalog.calls.vcf
gstacks/catalog.fa.gz
denovo_map/popmap_cstacks.tsv
name
Test-4 options_usage|input_type: vcf
popmap: denovo_map/popmap_cstacks.tsv
options_usage|input_vcf: gstacks/catalog.calls.vcf
add_log: True
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
gstacks/catalog.calls.vcf
denovo_map/popmap_cstacks.tsv
name
Test-5 options_filtering|filter_haplotype_wise: True
options_usage|input_type: stacks
options_filtering|min_samples_overall: 0.01
options_filtering|max_obs_het: 0.8
add_log: True
options_filtering|blacklist: populations/blacklist.tsv
popmap: denovo_map/popmap_cstacks.tsv
options_filtering|minperc: 0.1
options_usage|input_aln: list collection
options_filtering|min_mac: 1
options_filtering|min_maf: 0.01
options_filtering|minpop: 2
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
gstacks/catalog.calls.vcf
gstacks/catalog.fa.gz
denovo_map/popmap_cstacks.tsv
populations/blacklist.tsv
name
Test-6 options_usage|input_type: stacks
options_filtering|min_samples_overall: 0.01
popmap: denovo_map/popmap_cstacks.tsv
add_log: True
options_filtering|blacklist: populations/blacklist.tsv
options_filtering|max_obs_het: 0.8
options_filtering|filter_single_snp: --write_single_snp
options_filtering|minperc: 0.1
options_usage|input_aln: list collection
options_filtering|min_mac: 1
options_filtering|min_maf: 0.01
options_filtering|minpop: 2
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
gstacks/catalog.calls.vcf
gstacks/catalog.fa.gz
denovo_map/popmap_cstacks.tsv
populations/blacklist.tsv
name
Test-7 options_usage|input_type: stacks
add_log: True
merge_phase|merge_sites: True
popmap: denovo_map/popmap_cstacks.tsv
merge_phase|merge_prune_lim: 0.9
merge_phase|enzyme: ecoRI
options_usage|input_aln: list collection
locus_stats|hwe: True
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
gstacks/catalog.calls.vcf
gstacks/catalog.fa.gz
denovo_map/popmap_cstacks.tsv
name
Test-8 options_usage|input_type: stacks
fstats_conditional|correction_select|fst_correction: bonferroni_gen
kernel_smoothing|options_kernel|kernel: -k
add_log: True
fstats_conditional|correction_select|p_value_cutoff: 0.01
popmap: denovo_map/popmap_cstacks.tsv
fstats_conditional|fstats: yes
kernel_smoothing|bootstrap_reps: 23
options_usage|input_aln: list collection
kernel_smoothing|options_kernel|sigma: 150001
kernel_smoothing|bootstrap_resampling_mode|bootstrap: --bootstrap
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
refmap/catalog.calls.vcf
refmap/catalog.fa.gz
denovo_map/popmap_cstacks.tsv
name