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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 12:57:49 +0000
parents d3482e14d5a4
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d3482e14d5a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
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1 <tool id="vcfhethom" name="VCFhetHomAlleles:" version="@WRAPPER_VERSION@+galaxy0">
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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"/>
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7 <expand macro="stdio" />
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8 <command>
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9 #if str($analysis_type) == "count":
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31712f1ff0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom commit 36e9065027cc7bf721e9d203208477ee88906c57"
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10 vcfhetcount '${vcf_input}' > '${out_file1}'
31712f1ff0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom commit 36e9065027cc7bf721e9d203208477ee88906c57"
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11 #elif str($analysis_type) == "ratio":
31712f1ff0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom commit 36e9065027cc7bf721e9d203208477ee88906c57"
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12 vcfhethomratio '${vcf_input}' > '${out_file1}'
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4d7bf6277295 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfhethom commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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13 #elif str($analysis_type) == "allele_count":
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31712f1ff0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom commit 36e9065027cc7bf721e9d203208477ee88906c57"
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14 vcfcountalleles '${vcf_input}' > '${out_file1}'
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15 #end if
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16 </command>
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17 <inputs>
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18 <param name="analysis_type" type="select" display="radio" label="Select type of calculation:">
4d7bf6277295 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfhethom commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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19 <option value="count">Compute the number of heterozygotes</option>
4d7bf6277295 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfhethom commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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20 <option value="ratio">Compute the ratio between heterozygotes and homozygotes</option>
4d7bf6277295 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfhethom commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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21 <option value="allele_count">Compute the total number of alleles</option>
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22 </param>
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23 <param format="vcf" name="vcf_input" type="data" label="In this VCF dataset"/>
4d7bf6277295 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfhethom commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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24 </inputs>
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25 <outputs>
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26 <data format="tabular" name="out_file1" />
4d7bf6277295 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfhethom commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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27 </outputs>
4d7bf6277295 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfhethom commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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28 <tests>
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29 <test>
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30 <param name="analysis_type" value="count"/>
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31 <param name="vcf_input" value="vcflib.vcf"/>
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32 <output name="out_file1" file="vcfhethom-test1.tab"/>
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33 </test>
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34 <test>
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35 <param name="analysis_type" value="ratio"/>
4d7bf6277295 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfhethom commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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36 <param name="vcf_input" value="vcflib.vcf"/>
4d7bf6277295 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfhethom commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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37 <output name="out_file1" file="vcfhethom-test2.tab"/>
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38 </test>
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39 <test>
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40 <param name="analysis_type" value="allele_count"/>
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41 <param name="vcf_input" value="vcflib.vcf"/>
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42 <output name="out_file1" file="vcfhethom-test3.tab"/>
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43 </test>
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44 </tests>
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45 <help>
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46
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47 This tool performs three basic calculations:
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48
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49 (1) Computes the number of heterozygotes
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50 (2) Computes the ratio between heterozygotes and homozygotes
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51 (3) Computes the total number of alleles in the input dataset
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52
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53 ----
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54
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55 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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56
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57 </help>
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58 <expand macro="citations" />
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59 </tool>