Mercurial > repos > anton > vcfhethom
annotate vcfhethom.xml @ 3:5731e8c3ffde draft default tip
Uploaded
| author | anton |
|---|---|
| date | Mon, 15 Sep 2014 14:52:32 -0400 |
| parents | efba18d7b34b |
| children |
| rev | line source |
|---|---|
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2
efba18d7b34b
Updated tool version to 0.0.2
Anton Nekrutenko <anton@bx.psu.edu>
parents:
1
diff
changeset
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1 <tool id="vcfhethom" name="VCFhetHomAlleles:" version="0.0.2"> |
| 0 | 2 <requirements> |
| 3 | 3 <requirement type="package" version="8a5602bf07">vcflib</requirement> |
| 0 | 4 </requirements> |
| 5 <description>Count the number of heterozygotes and alleles, compute het/hom ratio</description> | |
| 6 <command> | |
| 7 | |
| 8 #if str($analysis_type) == "count": | |
| 9 vcfhetcount "${vcf_input}" > "${out_file1}" | |
| 10 #elif str($analysis_type) == "ratio": | |
| 11 vcfhethomratio "${vcf_input}" > "${out_file1}" | |
| 12 #elif str($analysis_type) == "allele_count": | |
| 13 vcfcountalleles "${vcf_input}" > "${out_file1}" | |
| 14 #end if | |
| 15 | |
| 16 </command> | |
| 17 | |
| 18 <inputs> | |
| 19 <param name="analysis_type" type="select" display="radio" label="Select type of calculation:"> | |
| 20 <option value="count">Compute the number of heterozygotes</option> | |
| 21 <option value="ratio">Compute the ratio between heterozygotes and homozygotes</option> | |
| 22 <option value="allele_count">Compute the total number of alleles</option> | |
| 23 </param> | |
| 24 <param format="vcf" name="vcf_input" type="data" label="In this VCF dataset"/> | |
| 25 </inputs> | |
| 26 <outputs> | |
| 27 <data format="tabular" name="out_file1" /> | |
| 28 </outputs> | |
| 29 <tests> | |
| 30 <test> | |
| 31 <param name="analysis_type" value="count"/> | |
| 32 <param name="vcf_input" value="vcflib.vcf"/> | |
| 33 <output name="out_file1" file="vcfhethom-test1.tab"/> | |
| 34 </test> | |
| 35 <test> | |
| 36 <param name="analysis_type" value="ratio"/> | |
| 37 <param name="vcf_input" value="vcflib.vcf"/> | |
| 38 <output name="out_file1" file="vcfhethom-test2.tab"/> | |
| 39 </test> | |
| 40 <test> | |
| 41 <param name="analysis_type" value="allele_count"/> | |
| 42 <param name="vcf_input" value="vcflib.vcf"/> | |
| 43 <output name="out_file1" file="vcfhethom-test3.tab"/> | |
| 44 </test> | |
| 45 </tests> | |
| 46 <help> | |
| 47 | |
| 48 This tool performs three basic calculations: | |
| 49 | |
| 50 (1) Computes the number of heterozygotes | |
| 51 (2) Computes the ratio between heterozygotes and homozygotes | |
| 52 (3) Computes the total number of alleles in the input dataset | |
| 53 | |
| 54 ---- | |
| 55 | |
| 56 This tools is based on vcfhetcount, vcfhethomratio,and vcfcountalleles utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
| 57 | |
| 58 </help> | |
| 59 </tool> |