Mercurial > repos > iuc > snpsift

annotate snpSift_annotate.xml @ 6:2b3e65a4252f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 693e1a3641c776965f68d688c8e1409adba7da1e
author iuc
date Wed, 16 Jan 2019 15:35:26 -0500
parents 09d6806c609e
children 5fab4f81391d
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1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.galaxy1">
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2 <description>SNPs from dbSnp</description>
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3 <!--
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4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
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5 -->
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6 <macros>
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7 <import>snpSift_macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="stdio" />
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11 <expand macro="version_command" />
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12 <command><![CDATA[
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13 SnpSift -Xmx8G annotate
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14 ${annotate.no_info}
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15 #if str($annotate.info_ids).strip():
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16 -info '$annotate.info_ids'
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17 #end if
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18 -q '$dbSnp' '$input' > '$output'
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19 ]]></command>
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20 <inputs>
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21 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
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22 <param name="dbSnp" type="data" format="vcf" label="VCF File with ID field annotated (e.g. dbSNP.vcf)"
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23 help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
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24 <conditional name="annotate">
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25 <param name="no_info" type="select" label="Fields to annotate">
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26 <option value="-noInfo">Only annotate ID field (no INFO fields will be added)</option>
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27 <option value="">Add also INFO fields</option>
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28 </param>
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29 <when value="-noInfo">
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30 <param name="info_ids" type="hidden" value="" />
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31 </when>
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32 <when value="">
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33 <param name="info_ids" type="text" value="" label="Limit INFO annotation to these INFO IDs" help="List is a comma separated list of fields. When blank, all INFO fields are included">
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34 <validator type="regex" message="IDs separated by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
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35 </param>
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36 </when>
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37 </conditional>
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38 </inputs>
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39 <outputs>
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40 <data name="output" format="vcf" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="input" ftype="vcf" value="annotate_1.vcf"/>
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45 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
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46 <conditional name="annotate">
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47 <param name="no_info" value=""/>
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48 </conditional>
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49 <output name="output">
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50 <assert_contents>
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51 <has_line_matching expression="1&#009;872687&#009;rs76166080&#009;C&#009;G&#009;.&#009;.&#009;.+;.+" />
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52 </assert_contents>
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53 </output>
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54 </test>
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55 <test>
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56 <param name="input" ftype="vcf" value="annotate_1.vcf"/>
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57 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
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58 <conditional name="annotate">
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59 <param name="no_info" value=""/>
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60 <param name="info_ids" value="dbSNPBuildID" />
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61 </conditional>
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62 <output name="output">
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63 <assert_contents>
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64 <has_line_matching expression="1&#009;872687&#009;rs76166080&#009;C&#009;G&#009;.&#009;.&#009;dbSNPBuildID=137" />
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65 </assert_contents>
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66 </output>
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67 </test>
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68 <test>
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69 <param name="input" ftype="vcf" value="annotate_1.vcf"/>
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70 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
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71 <conditional name="annotate">
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72 <param name="no_info" value="-noInfo"/>
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73 </conditional>
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74 <output name="output">
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75 <assert_contents>
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76 <has_line line="1&#009;872687&#009;rs76166080&#009;C&#009;G&#009;.&#009;.&#009;." />
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77 </assert_contents>
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78 </output>
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82 This is typically used to annotate IDs from dbSnp.
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83
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84 Annotating only the ID field from dbSnp137.vcf ::
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85
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86 Input VCF:
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87 CHROM POS ID REF ALT QUAL FILTER INFO
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88 22 16157571 . T G 0.0 FAIL NS=53
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89 22 16346045 . T C 0.0 FAIL NS=244
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90 22 16350245 . C A 0.0 FAIL NS=192
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91
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92 Annotated Output VCF:
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93 #CHROM POS ID REF ALT QUAL FILTER INFO
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94 22 16157571 . T G 0.0 FAIL NS=53
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95 22 16346045 rs56234788 T C 0.0 FAIL NS=244
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96 22 16350245 rs2905295 C A 0.0 FAIL NS=192
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97
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98 Annotating both the ID and INFO fields from dbSnp137.vcf ::
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99
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100 Input VCF:
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101 #CHROM POS ID REF ALT QUAL FILTER INFO
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102 22 16157571 . T G 0.0 FAIL NS=53
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103 22 16346045 . T C 0.0 FAIL NS=244
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104 22 16350245 . C A 0.0 FAIL NS=192
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105
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106 Annotated Output VCF:
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107 #CHROM POS ID REF ALT QUAL FILTER INFO
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108 22 16157571 . T G 0.0 FAIL NS=53
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109 22 16346045 rs56234788 T C 0.0 FAIL NS=244;RSPOS=16346045;GMAF=0.162248628884826;dbSNPBuildID=129;SSR=0;SAO=0;VP=050100000000000100000100;WGT=0;VC=SNV;SLO;GNO
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110 22 16350245 rs2905295 C A 0.0 FAIL NS=192;RSPOS=16350245;GMAF=0.230804387568556;dbSNPBuildID=101;SSR=1;SAO=0;VP=050000000000000100000140;WGT=0;VC=SNV;GNO
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111
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112 @EXTERNAL_DOCUMENTATION@
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113 - http://snpeff.sourceforge.net/SnpSift.html#annotate
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114 ]]></help>
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115 <expand macro="citations" />
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116 </tool>