Mercurial > repos > devteam > vcffilter
comparison vcffilter.xml @ 2:2d3c06c7e1f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
| author | devteam |
|---|---|
| date | Thu, 15 Sep 2016 16:05:48 -0400 |
| parents | e729e584cd6f |
| children | 952059348a30 |
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| 1:e729e584cd6f | 2:2d3c06c7e1f9 |
|---|---|
| 1 <tool id="vcffilter2" name="VCFfilter:" version="0.0.3"> | 1 <tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@.0"> |
| 2 <description>filter VCF data in a variety of attributes</description> | 2 <description>filter VCF data in a variety of attributes</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"> | 6 <expand macro="requirements"> |
| 7 <requirement type="package" version="0.2.6">tabix</requirement> | 7 <requirement type="package" version="1.3">htslib</requirement> |
| 8 </expand> | 8 <requirement type="package" version="0.2.6">tabix</requirement> |
| 9 <expand macro="stdio" /> | 9 </expand> |
| 10 <command> | 10 <expand macro="stdio" /> |
| 11 <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg --> | 11 <command> |
| 12 ln -s "${input1}" input1.vcf && | 12 <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg --> |
| 13 bgzip input1.vcf && | 13 ln -s "${input1}" input1.vcf && |
| 14 tabix -p vcf input1.vcf.gz && | 14 bgzip input1.vcf && |
| 15 vcffilter ${filterList} input1.vcf.gz > "${out_file1}" | 15 tabix -p vcf input1.vcf.gz && |
| 16 </command> | 16 vcffilter ${filterList} input1.vcf.gz > "${out_file1}" |
| 17 | 17 </command> |
| 18 <inputs> | |
| 19 <param name="filterList" type="text" value="-f "DP > 10"" label="Specify filterting expression" help="See explanation of filtering options below"> | |
| 20 <sanitizer> | |
| 21 <valid initial="string.printable"> | |
| 22 <remove value="'"/> | |
| 23 </valid> | |
| 24 <mapping initial="none"> | |
| 25 <add source="'" target="__sq__"/> | |
| 26 </mapping> | |
| 27 </sanitizer> | |
| 28 </param> | |
| 29 <param format="vcf" name="input1" type="data" label="VCF dataset to filter"> | |
| 30 </param> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data format="vcf" name="out_file1" /> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="filterList" value="-f "DP > 10""/> | |
| 38 <param name="input1" value="vcflib.vcf"/> | |
| 39 <output name="out_file1" file="vcffilter-test1.vcf"/> | |
| 40 </test> | |
| 41 </tests> | |
| 42 <help> | |
| 43 | 18 |
| 19 <inputs> | |
| 20 <param name="filterList" type="text" value="-f "DP > 10"" label="Specify filterting expression" help="See explanation of filtering options below"> | |
| 21 <sanitizer> | |
| 22 <valid initial="string.printable"> | |
| 23 <remove value="'"/> | |
| 24 </valid> | |
| 25 <mapping initial="none"> | |
| 26 <add source="'" target="__sq__"/> | |
| 27 </mapping> | |
| 28 </sanitizer> | |
| 29 </param> | |
| 30 <param format="vcf" name="input1" type="data" label="VCF dataset to filter"/> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data format="vcf" name="out_file1" /> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="filterList" value="-f "DP > 10""/> | |
| 38 <param name="input1" value="vcflib.vcf"/> | |
| 39 <output name="out_file1" file="vcffilter-test1.vcf"/> | |
| 40 </test> | |
| 41 </tests> | |
| 42 <help> | |
| 44 You can specify the following options within the **Specify filtering expression** box in any combination:: | 43 You can specify the following options within the **Specify filtering expression** box in any combination:: |
| 45 | 44 |
| 46 -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter | 45 -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter |
| 47 -g, --genotype-filter specifies a filter to apply to the genotype fields of records | 46 -g, --genotype-filter specifies a filter to apply to the genotype fields of records |
| 48 -s, --filter-sites filter entire records, not just alleles | 47 -s, --filter-sites filter entire records, not just alleles |
| 58 | 57 |
| 59 -f "DP > 10" # for info fields | 58 -f "DP > 10" # for info fields |
| 60 -g "GT = 1|1" # for genotype fields | 59 -g "GT = 1|1" # for genotype fields |
| 61 -f "CpG" # for 'flag' fields | 60 -f "CpG" # for 'flag' fields |
| 62 | 61 |
| 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. | 62 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. |
| 64 | 63 |
| 65 Operators can be any of: =, !, <, >, pipe, & | 64 Operators can be any of: =, !, <, >, pipe, & |
| 66 | 65 |
| 67 | 66 |
| 68 To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f):: | 67 To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f):: |
| 71 -r chrX # only output call on chromosome X | 70 -r chrX # only output call on chromosome X |
| 72 | 71 |
| 73 ----- | 72 ----- |
| 74 | 73 |
| 75 Vcffilter @IS_PART_OF_VCFLIB@ | 74 Vcffilter @IS_PART_OF_VCFLIB@ |
| 76 </help> | 75 </help> |
| 77 <expand macro="citations" /> | 76 <expand macro="citations" /> |
| 78 </tool> | 77 </tool> |