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1 <tool id="vcfhethom" name="VCFhetHomAlleles:" version="0.0.3">
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2 <description>Count the number of heterozygotes and alleles, compute het/hom ratio</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"></expand>
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7 <expand macro="stdio" />
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8 <command>
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9
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10 #if str($analysis_type) == "count":
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11 vcfhetcount "${vcf_input}" > "${out_file1}"
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12 #elif str($analysis_type) == "ratio":
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13 vcfhethomratio "${vcf_input}" > "${out_file1}"
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14 #elif str($analysis_type) == "allele_count":
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15 vcfcountalleles "${vcf_input}" > "${out_file1}"
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16 #end if
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17
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18 </command>
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19
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20 <inputs>
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21 <param name="analysis_type" type="select" display="radio" label="Select type of calculation:">
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22 <option value="count">Compute the number of heterozygotes</option>
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23 <option value="ratio">Compute the ratio between heterozygotes and homozygotes</option>
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24 <option value="allele_count">Compute the total number of alleles</option>
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25 </param>
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26 <param format="vcf" name="vcf_input" type="data" label="In this VCF dataset"/>
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27 </inputs>
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28 <outputs>
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29 <data format="tabular" name="out_file1" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="analysis_type" value="count"/>
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34 <param name="vcf_input" value="vcflib.vcf"/>
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35 <output name="out_file1" file="vcfhethom-test1.tab"/>
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36 </test>
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37 <test>
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38 <param name="analysis_type" value="ratio"/>
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39 <param name="vcf_input" value="vcflib.vcf"/>
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40 <output name="out_file1" file="vcfhethom-test2.tab"/>
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41 </test>
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42 <test>
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43 <param name="analysis_type" value="allele_count"/>
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44 <param name="vcf_input" value="vcflib.vcf"/>
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45 <output name="out_file1" file="vcfhethom-test3.tab"/>
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46 </test>
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47 </tests>
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48 <help>
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49
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50 This tool performs three basic calculations:
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51
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52 (1) Computes the number of heterozygotes
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53 (2) Computes the ratio between heterozygotes and homozygotes
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54 (3) Computes the total number of alleles in the input dataset
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55
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56 ----
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57
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58 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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59
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60 </help>
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61 <expand macro="citations" />
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62 </tool>
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