Mercurial > repos > iuc > snpsift

annotate snpSift_annotate.xml @ 17:ede8954f5c82 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
author iuc
date Wed, 18 Apr 2018 07:28:34 -0400
parents f0e87bdad733
children 0b0035e38abe
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17
ede8954f5c82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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1 <tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.galaxy0">
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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 #if $annotate.id == 'id':
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15 -id
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16 #elif str($annotate.info_ids).strip() != '':
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17 -info "$annotate.info_ids"
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18 #end if
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19 -q '$dbSnp' '$input' > '$output'
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20 ]]></command>
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21 <inputs>
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22 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
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23 <param name="dbSnp" type="data" format="vcf" label="VCF File with ID field annotated (e.g. dbSNP.vcf)"
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24 help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
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25 <conditional name="annotate">
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26 <param name="id" type="select" label="Fields to annotate">
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27 <option value="id">Only annotate ID field (no INFO fields will be added)</option>
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28 <option value="info">Add also INFO fields</option>
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29 </param>
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30 <when value="id"/>
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31 <when value="info">
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32 <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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33 <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
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34 </param>
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35 </when>
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <data name="output" format="vcf" />
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="input" ftype="vcf" value="annotate_1.vcf"/>
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44 <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
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45 <param name="id" value="id"/>
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46 <output name="output">
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47 <assert_contents>
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48 <has_text text="rs76166080" />
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49 </assert_contents>
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50 </output>
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54 This is typically used to annotate IDs from dbSnp.
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55
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56 Annotatating only the ID field from dbSnp137.vcf ::
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57
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58 Input VCF:
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59 CHROM POS ID REF ALT QUAL FILTER INFO
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60 22 16157571 . T G 0.0 FAIL NS=53
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61 22 16346045 . T C 0.0 FAIL NS=244
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62 22 16350245 . C A 0.0 FAIL NS=192
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63
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64 Annotated Output VCF:
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65 #CHROM POS ID REF ALT QUAL FILTER INFO
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66 22 16157571 . T G 0.0 FAIL NS=53
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67 22 16346045 rs56234788 T C 0.0 FAIL NS=244
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68 22 16350245 rs2905295 C A 0.0 FAIL NS=192
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69
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70 Annotatating both the ID and INFO fields from dbSnp137.vcf ::
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71
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72 Input VCF:
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73 #CHROM POS ID REF ALT QUAL FILTER INFO
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74 22 16157571 . T G 0.0 FAIL NS=53
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75 22 16346045 . T C 0.0 FAIL NS=244
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76 22 16350245 . C A 0.0 FAIL NS=192
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77
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78 Annotated Output VCF:
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79 #CHROM POS ID REF ALT QUAL FILTER INFO
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80 22 16157571 . T G 0.0 FAIL NS=53
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81 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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82 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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83
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84 @EXTERNAL_DOCUMENTATION@
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85 - http://snpeff.sourceforge.net/SnpSift.html#annotate
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86 ]]></help>
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87 <expand macro="citations" />
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88 </tool>