Mercurial > repos > miller-lab > genome_diversity
view nucleotide_diversity_pi.xml @ 34:f739a296a339
Update to Miller Lab devshed revision 09dc81dbebc5
author | Richard Burhans <burhans@bx.psu.edu> |
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date | Mon, 23 Sep 2013 13:37:19 -0400 |
parents | a631c2f6d913 |
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<tool id="gd_nucleotide_diversity_pi" name="Nucleotide Diversity" version="1.0.0"> <description>: &pi; and &theta;</description> <command interpreter="python"> #import json #import base64 #import zlib #set $ind_names = $snps.dataset.metadata.individual_names #set $ind_colms = $snps.dataset.metadata.individual_columns #set $ind_dict = dict(zip($ind_names, $ind_colms)) #set $ind_json = json.dumps($ind_dict, separators=(',',':')) #set $ind_comp = zlib.compress($ind_json, 9) #set $ind_arg = base64.b64encode($ind_comp) nucleotide_diversity_pi.py '$saps' '$snps' '$intervals' '$indivs' '$output' '$ind_arg' </command> <inputs> <param name="saps" type="data" format="gd_sap" label="SAP Dataset" /> <param name="snps" type="data" format="gd_snp" label="SNP Dataset" /> <param name="intervals" type="data" format="gd_covered_cds" label="Covered intervals" /> <param name="indivs" type="data" format="gd_indivs" label="Population individuals" /> </inputs> <outputs> <data name="output" format="txt" /> </outputs> <requirements> <requirement type="package" version="0.1">gd_c_tools</requirement> </requirements> <help> **What it does** This tool computes values that estimate some basic parameters. **Output** the number of nonsyn SNPs, total number of nonsynon sites, piNon, the number of synon SNPs, total number of synon sites, piSyn, plus total length of covered intervals, thetaNon, thetaSyn </help> </tool>