Repository revision
7:1fa3942bec04

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

Calculate alpha diversity tool metadata
Miscellaneous
on each sample in an otu table, using a variety of alpha diversity metrics (alpha_diversity)
qiime_alpha_diversity
toolshed.g2.bx.psu.edu/repos/iuc/qiime_alpha_diversity/qiime_alpha_diversity/1.9.1.0
1.9.1.0
alpha_diversity.py --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/qiime_alpha_diversity/qiime_alpha_diversity/1.9.1.0 (this tool)
qiime_alpha_diversity
Requirements (dependencies defined in the <requirements> tag set)
name version type
qiime 1.9.1 package
Functional tests
name inputs outputs required files
Test-1 input_path: alpha_diversity/otu_table.biom
attributes: name
alpha_diversity/otu_table.biom
name
Test-2 metrics: ['ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'equitability', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'observed_otus', 'observed_species', 'osd', 'simpson_reciprocal', 'robbins', 'shannon', 'simpson', 'simpson_e', 'singles', 'strong', 'PD_whole_tree']
tree_path: alpha_diversity/rep_set.tre
input_path: alpha_diversity/otu_table.biom
attributes: name
alpha_diversity/otu_table.biom
alpha_diversity/rep_set.tre
name