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1 <tool id="vcf2tsv" name="VCFtoTab-delimited:" version="0.0.2">
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2 <requirements>
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3 <requirement type="package" version="8a5602bf07">vcflib</requirement>
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4 </requirements>
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5 <description>Convert VCF data into TAB-delimited format</description>
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6 <command>vcf2tsv ${g_option} -n "${null_filler}" "${input}" > "${out_file1}"</command>
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7 <inputs>
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8 <param format="vcf" name="input" type="data" label="Select VCF dataset to convert"/>
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9 <param name="g_option" type="boolean" checked="true" truevalue="-g" falsevalue="" label="Report data per sample" help="-g option"/>
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10 <param name="null_filler" type="select" label="Fill empty fields with" help="-n option" >
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11 <option value="">Nothing</option>
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12 <option value=".">.</option>
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13 <option value="*">*</option>
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14 <option value="NULL">NULL</option>
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15 </param>
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16 </inputs>
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17 <outputs>
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18 <data format="tabular" name="out_file1" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="g_option" value="true"/>
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23 <param name="null_filler" value="."/>
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24 <param name="input" value="vcflib.vcf"/>
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25 <output name="out_file1" file="vcf2tsv-test1.tab"/>
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26 </test>
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27 <test>
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28 <param name="g_option" value="false"/>
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29 <param name="null_filler" value="."/>
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30 <param name="input" value="vcflib.vcf"/>
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31 <output name="out_file1" file="vcf2tsv-test2.tab"/>
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32 </test>
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33 </tests>
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34 <help>
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35
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36 Converts VCF dataset to tab-delimited format, using null string to replace empty values in the table.
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37 Specifying "**Report data per sample**" (-g) will output one line per sample with genotype information.
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38
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39 ----
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40
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41 Vcf2Tsv is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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42
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43 </help>
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44 </tool>
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