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1 <tool id="vt_@BINARY@" name="VT @BINARY@" version="@VERSION@.0">
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2 <description>normalizes variants in a VCF file</description>
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <macros>
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6 <import>vt_macros.xml</import>
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7 <token name="@BINARY@">normalize</token>
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8 </macros>
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9 <command>
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10 <![CDATA[
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11 vt @BINARY@
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12 -o "${ outfile }"
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13 ##-q do not print options and summary []
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14 -w window size for local sorting of variants [10000]
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15 -I $intervals_file
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16 ##-i intervals []
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17 -r $reference_genome
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18 "${ infile }"
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19 ]]>
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20 </command>
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21 <expand macro="stdio" />
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22 <inputs>
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1
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23 <param name="infile" type="data" format="vcf" label="VCF file to be normalised" />
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0
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24
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25 <param name="reference_genome" type="select" label="Using reference genome">
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26 <options from_data_table="fasta_indexes">
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27 <filter type="data_meta" ref="infile" key="dbkey" column="1" />
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28 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
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29 </options>
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30 </param>
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31
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32 <param name="intervals_file" type="data" format="bed" optional="True" label="File containing list of intervals" />
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33 <param name="window" type="integer" value="10000" size="10" label="Window size for local sorting of variants"
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34 help="(-w)">
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35 <validator type="in_range" min="0"/>
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36 </param>
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37
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38 </inputs>
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39 <outputs>
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40 <data name="outfile" format="vcf" label="${tool.name} on ${on_string}" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 </test>
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45 </tests>
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46 <help>
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47 **What it does**
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48
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49 Normalize variants in a VCF file. Normalized variants may have their positions changed; in such cases,
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50 the normalized variants are reordered and output in an ordered fashion. The local reordering takes place over a window of 10000 base pairs.
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51
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52 @CITATION@
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53 </help>
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54 <!--expand macro="citations"/-->
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55 </tool>
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