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annotate nucleotide_diversity_pi.xml @ 27:8997f2ca8c7a

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Update to Miller Lab devshed revision bae0d3306d3b
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 15 Jul 2013 10:47:35 -0400
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1 <tool id="gd_nucleotide_diversity_pi" name="Nucleotide Diversity" version="1.0.0">
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2 <description>: &amp;pi; and &amp;theta;</description>
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3
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4 <command interpreter="python">
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5 #import json
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6 #import base64
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7 #import zlib
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8 #set $ind_names = $snps.dataset.metadata.individual_names
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9 #set $ind_colms = $snps.dataset.metadata.individual_columns
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10 #set $ind_dict = dict(zip($ind_names, $ind_colms))
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11 #set $ind_json = json.dumps($ind_dict, separators=(',',':'))
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12 #set $ind_comp = zlib.compress($ind_json, 9)
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13 #set $ind_arg = base64.b64encode($ind_comp)
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14 nucleotide_diversity_pi.py '$saps' '$snps' '$intervals' '$indivs' '$output' '$ind_arg'
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15 </command>
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16
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17 <inputs>
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18 <param name="saps" type="data" format="gd_sap" label="SAP Dataset" />
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19 <param name="snps" type="data" format="gd_snp" label="SNP Dataset" />
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20 <param name="intervals" type="data" format="gd_covered_cds" label="Covered intervals" />
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21 <param name="indivs" type="data" format="gd_indivs" label="Population individuals" />
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22 </inputs>
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23
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24 <outputs>
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25 <data name="output" format="txt" />
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26 </outputs>
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27
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28 <help>
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29 **What it does**
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30
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31 This tool computes values that estimate some basic parameters.
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32
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33 **Output**
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34
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35 the number of nonsyn SNPs, total number of nonsynon sites, piNon,
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36 the number of synon SNPs, total number of synon sites, piSyn, plus
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37 total length of covered intervals, thetaNon, thetaSyn
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38 </help>
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39 </tool>