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comparison nucleotide_diversity_pi.xml @ 22:95a05c1ef5d5

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update to devshed revision aaece207bd01
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 11 Mar 2013 11:28:06 -0400
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21:d6b961721037 22:95a05c1ef5d5
1 <tool id="gd_nucleotide_diversity_pi" name="Nucleotide Diversity" version="1.0.0">
2 <description>: &amp;pi; and &amp;theta;</description>
3
4 <command interpreter="python">
5 nucleotide_diversity_pi.py "$saps" "$snps" "$intervals" "$indivs" "$output"
6 #for $individual_name, $individual_col in zip($snps.dataset.metadata.individual_names, $snps.dataset.metadata.individual_columns)
7 #set $arg = '%s:%s' % ($individual_col, $individual_name)
8 "$arg"
9 #end for
10 </command>
11
12 <inputs>
13 <param name="saps" type="data" format="gd_sap" label="SAP Dataset" />
14 <param name="snps" type="data" format="gd_snp" label="SNP Dataset" />
15 <param name="intervals" type="data" format="gd_covered_cds" label="Covered intervals" />
16 <param name="indivs" type="data" format="gd_indivs" label="Population individuals" />
17 </inputs>
18
19 <outputs>
20 <data name="output" format="txt" />
21 </outputs>
22
23 <help>
24 **What it does**
25
26 This tool computes values that estimate some basic parameters.
27
28 **Output**
29
30 the number of nonsyn SNPs, total number of nonsynon sites, piNon,
31 the number of synon SNPs, total number of synon sites, piSyn, plus
32 total length of covered intervals, thetaNon, thetaSyn
33 </help>
34 </tool>