Mercurial > repos > sanbi-uwc > vcf_to_alignment

annotate vcf_to_alignment.xml @ 4:f58178c0f00d draft

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planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
author sanbi-uwc
date Mon, 15 Oct 2018 00:34:44 -0400
parents 62fbd3f96b30
children 4f3f7d390382
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1 <?xml version="1.0" encoding="utf-8" ?>
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2 <tool id="vcf_to_alignment" name="Generate FASTA alignment from VCF collection" version="0.4">
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3 <description>Generate a multiple sequence alignment given a collection of variants and a reference sequence</description>
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4 <requirements>
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5 <requirement type="package" version="1.67">biopython</requirement>
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6 <requirement type="package" version="0.6.8">pyvcf</requirement>
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7 <requirement type="package" version="2.1.0">intervaltree</requirement>
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8 </requirements>
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9 <command detect_errors="aggressive"><![CDATA[
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10 #if str($reference.source) == 'history':
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11 ln -s '${reference.history}' reference.fasta &&
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12 #end if
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13 python $__tool_directory__/vcf_to_msa.py
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14 $remove_invariant_sites
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15 --vcf_files
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16 #for $vcf_file in $vcf_inputs:
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17 '${vcf_file.element_identifier}^^^${vcf_file}'
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18 #end for
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19 --reference_file
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20 #if str($reference.source) == 'history':
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21 reference.fasta
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22 #else
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23 '${reference.builtin.fields.path}'
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24 #end if
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25 #if $exclude_list.do_exclude == 'yes':
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26 --exclude $exclude_list.exclude_file
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27 #end if
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28 --output_file '${output_alignment}'
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29 ]]>
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30 </command>
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31 <inputs>
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32 <param name="vcf_inputs" type="data_collection" format="vcf" collection_type="list" label="Variants (VCF format)" />
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33 <param name="remove_invariant_sites" type="boolean" truevalue="--remove_invariant" falsevalue="" label="Remove invariant sites from alignment" />
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34 <conditional name="reference" label="Reference sequence source">
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35 <param name="source" type="select">
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36 <option value="history" selected="True">History</option>
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37 <option value="builtin">Built-in</option>
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38 </param>
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39 <when value="history">
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40 <param name="history" type="data" format="fasta" label="Reference sequence" />
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41 </when>
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42 <when value="builtin">
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43 <param name="builtin" type="select" label="Reference sequence (FASTA format)">
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44 <options from_data_table="all_fasta" />
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45 <validator type="no_options" message="No FASTA datasets are available for the selected input dataset" />
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46 </param>
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47 </when>
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48 </conditional>
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49 <conditional name="exclude_list">
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50 <param name="do_exclude" type="select">
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51 <option value="yes">Yes</option>
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52 <option value="no" selected="true">No</option>
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53 </param>
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54 <when value="yes">
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55 <param name="exclude_file" type="data" format="bed" label="BED file with regions to exclude" />
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56 </when>
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57 <when value="no"></when>
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58 </conditional>
0
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59 </inputs>
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60 <outputs>
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61 <data name="output_alignment" format="fasta" label="Alignment ${on_string}" />
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="remove_invariant_sites" value="False" />
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66 <param name="do_exclude" value="no" />
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67 <param name="vcf_inputs">
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68 <collection type="list">
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69 <element name="vcf_inputs.vcf1" value="vcf1.vcf" />
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70 <element name="vcf_inputs.vcf2" value="vcf2.vcf" />
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71 <element name="vcf_inputs.vcf3" value="vcf3.vcf" />
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72 </collection>
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73 </param>
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74 <param name="history" value="reference.fasta" ftype="fasta" />
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75 <output name="output_alignment" value="output1.fasta" />
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76 </test>
3
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77 <test>
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78 <param name="remove_invariant_sites" value="True" />
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79 <param name="do_exclude" value="no" />
3
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80 <param name="vcf_inputs">
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81 <collection type="list">
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82 <element name="vcf_inputs.vcf1" value="vcf1.vcf" />
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83 <element name="vcf_inputs.vcf2" value="vcf2.vcf" />
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84 <element name="vcf_inputs.vcf3" value="vcf3.vcf" />
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85 </collection>
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86 </param>
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87 <param name="history" value="reference.fasta" ftype="fasta" />
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88 <output name="output_alignment" value="output2.fasta" />
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89 </test>
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90 <test>
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91 <param name="remove_invariant_sites" value="True" />
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92 <param name="do_exclude" value="yes" />
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93 <param name="exclude_file" value="exclude1.bed" />
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94 <param name="vcf_inputs">
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95 <collection type="list">
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96 <element name="vcf_inputs.vcf1" value="vcf1.vcf" />
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97 <element name="vcf_inputs.vcf2" value="vcf2.vcf" />
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98 <element name="vcf_inputs.vcf3" value="vcf3.vcf" />
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99 </collection>
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100 </param>
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101 <param name="history" value="reference.fasta" ftype="fasta" />
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102 <output name="output_alignment" value="output3.fasta" />
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103 </test>
0
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104 </tests>
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105 <help><![CDATA[
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106 Using the SNPs identified by the VCF files given as input, generates a sequence including the
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107 SNPs by combining them with the reference and then combines the sequences into a FASTA
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108 format alignment file.
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109 ]]>
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110 </help>
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111 <citations></citations>
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112 </tool>