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1 <tool id="vcfselectsamples" name="VCFselectsamples:" version="0.0.3">
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2 <description>Select samples from a VCF dataset</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>vcfkeepsamples "${input1}" ${ ' '.join( map( lambda x:'"%s"' % ( x ), str($vcf_samples ).split(",") ) ) } > "${out_file1}"</command>
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9 <inputs>
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10 <param format="vcf" name="input1" type="data" label="Select VCF dataset" />
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11 <param name="vcf_samples" type="select" label="Check to keep samples; Uncheck to remove" display="checkboxes" multiple="true">
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12 <options>
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13 <filter type="data_meta" ref="input1" key="sample_names" />
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14 </options>
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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="vcf" 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="vcf_samples" value="NA00001,NA00003"/>
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23 <param name="input1" value="vcflib.vcf"/>
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24 <output name="out_file1" file="vcfselectsamples-test1.vcf"/>
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25 </test>
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26 </tests>
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27 <help>
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28
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29 Allows to keep or remove samples from a VCF file.
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30
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31 -----
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32
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33 .. class:: infomark
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34
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35
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36 **Example**:
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37
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38 Selecting *NA00001* and *NA00003* from the following VCF line::
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39
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40 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
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41 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
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42
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43 will, obviously, remove *NA00002*::
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44
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45 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00003
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46 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2/2:35:4:.,.
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47
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48 ----
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49
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50 Vcfselectsamples is based on vcfkeepsamples/vcfremovesamples utilities from **VCFlib** toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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51 </help>
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52 <expand macro="citations" />
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53 </tool>
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