Mercurial > repos > devteam > vcffilter
changeset 7:7ce3b93e0883 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
| author | iuc |
|---|---|
| date | Tue, 07 May 2019 11:59:01 -0400 |
| parents | 447c0f9c0a9b |
| children | af9bfb0f213e |
| files | test-data/vcffilter-test2.vcf vcffilter.xml |
| diffstat | 2 files changed, 36 insertions(+), 2 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcffilter-test2.vcf Tue May 07 11:59:01 2019 -0400 @@ -0,0 +1,26 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##filter="!( DP > 10 )" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> +##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency"> +##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"> +##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129"> +##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership"> +##FILTER=<ID=q10,Description="Quality below 10"> +##FILTER=<ID=s50,Description="Less than 50% of samples have data"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> +##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element"> +##ALT=<ID=CNV,Description="Copy number variable region"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,.
--- a/vcffilter.xml Thu May 02 18:33:20 2019 -0400 +++ b/vcffilter.xml Tue May 07 11:59:01 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy2"> +<tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy3"> <description>filter VCF data in a variety of attributes</description> <macros> <import>macros.xml</import> @@ -35,7 +35,7 @@ <option value="-f">Info filter (-f)</option> <option value="-g">Genotype filter (-g)</option> </param> - <param name="filter_value" type="text" value="DP > 10" label="Specify filterting value" help="See explanation of filtering options below"> + <param name="filter_value" type="text" value="DP > 10" label="Specify filtering value" help="See explanation of filtering options below"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> @@ -46,6 +46,7 @@ <add source=""" target=""/> </mapping> </sanitizer> + <validator type="expression" message="Invalid operator provided, valid operators are =, !, <, >, |, &.">value is not None and not any(x in value for x in ["<=", "=<", ">=", "=>"])</validator> </param> </repeat> <param name="filter_sites" argument="--filter-sites" type="boolean" truevalue="--filter-sites" falsevalue="" label="Filter entire records, not just alleles"/> @@ -67,6 +68,13 @@ <param name="input1" value="vcflib.vcf"/> <output name="out_file1" file="vcffilter-test1.vcf"/> </test> + <test> + <param name="filter_repeat_0|filter_type" value="-f"/> + <param name="filter_repeat_0|filter_value" value="!( DP > 10 )"/> + <param name="invert" value="true"/> + <param name="input1" value="vcflib.vcf"/> + <output name="out_file1" file="vcffilter-test2.vcf"/> + </test> </tests> <help><![CDATA[ You can specify the following options within the **Specify filtering expression** box in any combination::