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annotate nucleotide_diversity_pi.xml @ 24:248b06e86022

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Added gd_genotype datatype. Modified tools to support new datatype.
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 28 May 2013 16:24:19 -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 nucleotide_diversity_pi.py "$saps" "$snps" "$intervals" "$indivs" "$output"
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6 #for $individual_name, $individual_col in zip($snps.dataset.metadata.individual_names, $snps.dataset.metadata.individual_columns)
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7 #set $arg = '%s:%s' % ($individual_col, $individual_name)
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8 "$arg"
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9 #end for
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10 </command>
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11
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12 <inputs>
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13 <param name="saps" type="data" format="gd_sap" label="SAP Dataset" />
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14 <param name="snps" type="data" format="gd_snp" label="SNP Dataset" />
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15 <param name="intervals" type="data" format="gd_covered_cds" label="Covered intervals" />
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16 <param name="indivs" type="data" format="gd_indivs" label="Population individuals" />
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17 </inputs>
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18
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19 <outputs>
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20 <data name="output" format="txt" />
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21 </outputs>
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23 <help>
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24 **What it does**
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25
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26 This tool computes values that estimate some basic parameters.
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27
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28 **Output**
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29
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30 the number of nonsyn SNPs, total number of nonsynon sites, piNon,
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31 the number of synon SNPs, total number of synon sites, piSyn, plus
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32 total length of covered intervals, thetaNon, thetaSyn
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33 </help>
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34 </tool>