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1 <tool id="vcfhethom" name="VCFhetHomAlleles:" version="0.0.1">
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2 <requirements>
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3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
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4 </requirements>
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5 <description>Count the number of heterozygotes and alleles, compute het/hom ratio</description>
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6 <command>
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7
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8 #if str($analysis_type) == "count":
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9 vcfhetcount "${vcf_input}" > "${out_file1}"
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10 #elif str($analysis_type) == "ratio":
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11 vcfhethomratio "${vcf_input}" > "${out_file1}"
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12 #elif str($analysis_type) == "allele_count":
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13 vcfcountalleles "${vcf_input}" > "${out_file1}"
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14 #end if
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15
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16 </command>
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17
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18 <inputs>
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19 <param name="analysis_type" type="select" display="radio" label="Select type of calculation:">
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20 <option value="count">Compute the number of heterozygotes</option>
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21 <option value="ratio">Compute the ratio between heterozygotes and homozygotes</option>
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22 <option value="allele_count">Compute the total number of alleles</option>
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23 </param>
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24 <param format="vcf" name="vcf_input" type="data" label="In this VCF dataset"/>
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25 </inputs>
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26 <outputs>
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27 <data format="tabular" name="out_file1" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="analysis_type" value="count"/>
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32 <param name="vcf_input" value="vcflib.vcf"/>
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33 <output name="out_file1" file="vcfhethom-test1.tab"/>
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34 </test>
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35 <test>
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36 <param name="analysis_type" value="ratio"/>
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37 <param name="vcf_input" value="vcflib.vcf"/>
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38 <output name="out_file1" file="vcfhethom-test2.tab"/>
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39 </test>
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40 <test>
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41 <param name="analysis_type" value="allele_count"/>
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42 <param name="vcf_input" value="vcflib.vcf"/>
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43 <output name="out_file1" file="vcfhethom-test3.tab"/>
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44 </test>
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45 </tests>
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46 <help>
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47
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48 This tool performs three basic calculations:
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49
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50 (1) Computes the number of heterozygotes
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51 (2) Computes the ratio between heterozygotes and homozygotes
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52 (3) Computes the total number of alleles in the input dataset
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53
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54 ----
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55
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56 This tools is based on vcfhetcount, vcfhethomratio,and vcfcountalleles utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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57
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58 </help>
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59 </tool>
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