Mercurial > repos > bgruening > vt_normalize

annotate vt_normalize.xml @ 0:7c2ef0170f03 draft default tip

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planemo upload for repository https://github.com/atks/vt commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472-dirty
author bgruening
date Sat, 04 Jun 2016 12:44:06 -0400
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1 <tool id="vt_normalize" name="VT @BINARY@" version="@VERSION@.0">
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2 <description>normalizes variants in a VCF file</description>
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3 <macros>
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4 <import>vt_macros.xml</import>
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5 <token name="@BINARY@">normalize</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
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12 vt @BINARY@
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13 #if str($output_format) == 'bcf':
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14 -o normalised.bcf
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15 #else:
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16 -o normalised.vcf
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17 #end if
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18 ##-q do not print options and summary []
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19 -w $window
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20
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21 #if str( $intervals_file ) != 'None':
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22 -I "${intervals_file}"
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23 #end if
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24 $n
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25 ##-i intervals []
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26
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27 #if $reference_source.reference_source_selector != "history":
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28 -r "${reference_source.reference_genome.fields.path}"
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29 #else:
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30 -r "${reference_source.reference_genome}"
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31 #end if
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32
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33 "${ infile }"
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34
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35 &&
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36 ## For some reason, the file move will randomly produce empty files.
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37 ## Wait two seconds to let the system close file handlers and clean up.
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38 sleep 2
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39 &&
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40
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41 #if str($output_format) == 'bcf':
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42 mv normalised.bcf "${ outfile }";
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43 #else:
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44 mv normalised.vcf "${ outfile }";
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45 #end if
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46
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47 ]]>
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48 </command>
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49 <inputs>
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50 <param name="infile" type="data" format="vcf" label="VCF file to be normalised" />
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51
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52 <conditional name="reference_source">
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53 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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54 <option value="cached" selected="True">Locally cached</option>
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55 <option value="history">History</option>
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56 </param>
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57 <when value="cached">
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58 <param name="reference_genome" type="select" label="Using reference genome">
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59 <options from_data_table="fasta_indexes">
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60 <filter type="data_meta" ref="infile" key="dbkey" column="1" />
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61 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
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62 </options>
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63 </param>
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64 </when>
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65 <when value="history">
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66 <param name="reference_genome" type="data" format="fasta" label="Using reference file" />
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67 </when>
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68 </conditional>
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69 <param name="intervals_file" type="data" format="bed" optional="True" label="File containing list of intervals" />
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70 <param name="window" type="integer" value="10000" label="Window size for local sorting of variants"
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71 help="(-w)">
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72 <validator type="in_range" min="0"/>
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73 </param>
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74 <param argument="-n" type="boolean" truevalue="-n" falsevalue=""
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75 label="Do not fail when REF is inconsistent with reference sequence for non SNPs"
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76 help=""/>
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77 <param name="output_format" type="select" label="Choose the output format" help="">
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78 <option value="bcf">BCF</option>
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79 <option value="vcf" selected="true">VCF</option>
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80 </param>
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81 </inputs>
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82 <outputs>
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83 <data name="outfile" format="vcf" label="${tool.name} on ${on_string}">
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84 <change_format>
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85 <when input="output_format" value="bcf" format="bcf" />
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86 </change_format>
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87 </data>
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88 </outputs>
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89 <tests>
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90 <test>
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91 <param name="infile" value="infile01.vcf" />
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92 <param name="reference_source_selector" value="history" />
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93 <param name="reference_genome" value="20.fa.bz2" />
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94 <param name="n" value="True" />
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95 <output name="outfile" file="normalize_result01.vcf" ftype="vcf" />
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96 </test>
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97 </tests>
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98 <help>
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99 <![CDATA[
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100 **What it does**
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101
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102 Normalize variants in a VCF file. Normalized variants may have their positions changed; in such cases,
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103 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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104
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105 @CITATION@
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106 ]]>
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107 </help>
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108 <expand macro="citations"/>
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109 </tool>