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