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annotate vcffilter.xml @ 0:b71701c8b884 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:31:38 -0500
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b71701c8b884 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="vcffilter2" name="VCFfilter:" version="0.0.3">
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2 <description>filter VCF data in a variety of attributes</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="0.2.6">tabix</requirement>
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8 </expand>
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9 <expand macro="stdio" />
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10 <command>
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11 <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg -->
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12 ln -s "${input1}" input1.vcf &amp;&amp;
b71701c8b884 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 bgzip input1.vcf &amp;&amp;
b71701c8b884 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 tabix -p vcf input1.vcf.gz &amp;&amp;
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15 vcffilter ${filterList} input1.vcf.gz > "${out_file1}"
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16 </command>
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17
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18 <inputs>
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19 <param name="filterList" type="text" value="-f &quot;DP &gt; 10&quot;" label="Specify filterting expression" help="See explanation of filtering options below">
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20 <sanitizer>
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21 <valid initial="string.printable">
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22 <remove value="&apos;"/>
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23 </valid>
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24 <mapping initial="none">
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25 <add source="&apos;" target="__sq__"/>
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26 </mapping>
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27 </sanitizer>
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28 </param>
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29 <param format="vcf" name="input1" type="data" label="VCF dataset to filter">
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30 </param>
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31 </inputs>
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32 <outputs>
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33 <data format="vcf" name="out_file1" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="filterList" value="-f &quot;DP &gt; 10&quot;"/>
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38 <param name="input1" value="vcflib.vcf"/>
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39 <output name="out_file1" file="vcffilter-test1.vcf"/>
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40 </test>
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41 </tests>
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42 <help>
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43
b71701c8b884 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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44 You can specify the following options within the **Specify filtering expression** box in any combination::
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45
b71701c8b884 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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46 -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter
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47 -g, --genotype-filter specifies a filter to apply to the genotype fields of records
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48 -s, --filter-sites filter entire records, not just alleles
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49 -t, --tag-pass tag vcf records as positively filtered with this tag, print all records
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50 -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records
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51 -A, --append-filter append the existing filter tag, don't just replace it
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52 -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag
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53 -v, --invert inverts the filter, e.g. grep -v
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54 -o, --or use logical OR instead of AND to combine filters
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55 -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g)
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56
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57 Filters are specified in the form {ID} {operator} {value}::
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58
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59 -f "DP > 10" # for info fields
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60 -g "GT = 1|1" # for genotype fields
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61 -f "CpG" # for 'flag' fields
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62
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63 Any number of filters may be specified. They are combined via logical AND unless the --or option is specified. For convenience, you can specify "QUAL" to refer to the quality of the site, even though it does not appear in the INFO fields.
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64
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65 Operators can be any of: =, !, &lt;, &gt;, pipe, &amp;
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66
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67
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68 To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f)::
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69
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70 -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20
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71 -r chrX # only output call on chromosome X
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72
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73 -----
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74
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75 Vcffilter @IS_PART_OF_VCFLIB@
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76 </help>
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77 <expand macro="citations" />
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78 </tool>