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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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6
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12 #if str($output_format) == 'bcf':
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5
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13 -o normalised.bcf
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14 #else:
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15 -o normalised.vcf
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16 #end if
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0
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17 ##-q do not print options and summary []
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4
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18 -w $window
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3
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19
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20 #if str( $intervals_file ) != 'None':
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21 -I "${intervals_file}"
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22 #end if
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23
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0
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24 ##-i intervals []
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3
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25
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26 #if $reference_source.reference_source_selector != "history":
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4
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27 -r "${reference_source.reference_genome.fields.path}"
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3
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28 #else:
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29 -r "${reference_source.reference_genome}"
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30 #end if
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31
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6
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32 "${ infile }"
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5
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33
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6
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34 &&
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35
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36 #if str($output_format) == 'bcf':
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5
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37 mv normalised.bcf "${ outfile }";
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38 #else:
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39 mv normalised.vcf "${ outfile }";
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40 #end if
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41
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42 ]]>
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43 </command>
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44 <expand macro="stdio" />
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45 <inputs>
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1
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46 <param name="infile" type="data" format="vcf" label="VCF file to be normalised" />
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47
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3
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48
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49 <conditional name="reference_source">
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50 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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51 <option value="cached" selected="True">Locally cached</option>
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52 <option value="history">History</option>
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53 </param>
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54 <when value="cached">
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55 <param name="reference_genome" type="select" label="Using reference genome">
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56 <options from_data_table="fasta_indexes">
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57 <filter type="data_meta" ref="infile" key="dbkey" column="1" />
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58 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
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59 </options>
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60 </param>
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61 </when>
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62 <when value="history">
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63 <param name="reference_genome" type="data" format="fasta" label="Using reference file" />
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64 </when>
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65 </conditional>
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66
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67 <param name="intervals_file" type="data" format="bed" optional="True" label="File containing list of intervals" />
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68 <param name="window" type="integer" value="10000" size="10" label="Window size for local sorting of variants"
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69 help="(-w)">
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70 <validator type="in_range" min="0"/>
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71 </param>
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72
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5
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73 <param name="output_format" type="select" label="Choose the output format" help="">
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74 <option value="bcf">BCF</option>
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75 <option value="vcf" selected="true">VCF</option>
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76 </param>
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77
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0
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78 </inputs>
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79 <outputs>
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5
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80 <data name="outfile" format="vcf" label="${tool.name} on ${on_string}">
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81 <change_format>
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82 <when input="output_format" value="bcf" format="bcf" />
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83 </change_format>
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84 </data>
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0
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85 </outputs>
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86 <tests>
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87 <test>
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88 </test>
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89 </tests>
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90 <help>
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91 **What it does**
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92
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93 Normalize variants in a VCF file. Normalized variants may have their positions changed; in such cases,
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94 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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95
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96 @CITATION@
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97 </help>
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98 <!--expand macro="citations"/-->
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99 </tool>
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