Mercurial > repos > devteam > vcffilter
changeset 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 |
| files | macros.xml tool_dependencies.xml vcffilter.xml |
| diffstat | 3 files changed, 79 insertions(+), 88 deletions(-) [+] |
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--- a/macros.xml Wed Nov 11 12:59:23 2015 -0500 +++ b/macros.xml Thu Sep 15 16:05:48 2016 -0400 @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="8a5602bf07">vcflib</requirement> + <requirement type="package" version="1.0.0_rc1">vcflib</requirement> <yield/> </requirements> </xml> @@ -10,6 +10,7 @@ <exit_code range="1:" level="fatal" /> </stdio> </xml> + <token name="@WRAPPER_VERSION@">1.0.0_rc1</token> <xml name="citations"> <citations> <citation type="bibtex">
--- a/tool_dependencies.xml Wed Nov 11 12:59:23 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="vcflib" version="8a5602bf07"> - <repository changeset_revision="7e67466b033e" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="tabix" version="0.2.6"> - <repository changeset_revision="389d2376b60b" name="package_tabix_0_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>
--- a/vcffilter.xml Wed Nov 11 12:59:23 2015 -0500 +++ b/vcffilter.xml Thu Sep 15 16:05:48 2016 -0400 @@ -1,78 +1,77 @@ -<tool id="vcffilter2" name="VCFfilter:" version="0.0.3"> - <description>filter VCF data in a variety of attributes</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"> - <requirement type="package" version="0.2.6">tabix</requirement> - </expand> - <expand macro="stdio" /> - <command> - <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg --> - ln -s "${input1}" input1.vcf && - bgzip input1.vcf && - tabix -p vcf input1.vcf.gz && - vcffilter ${filterList} input1.vcf.gz > "${out_file1}" - </command> - - <inputs> - <param name="filterList" type="text" value="-f "DP > 10"" label="Specify filterting expression" help="See explanation of filtering options below"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - </valid> - <mapping initial="none"> - <add source="'" target="__sq__"/> - </mapping> - </sanitizer> - </param> - <param format="vcf" name="input1" type="data" label="VCF dataset to filter"> - </param> - </inputs> - <outputs> - <data format="vcf" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="filterList" value="-f "DP > 10""/> - <param name="input1" value="vcflib.vcf"/> - <output name="out_file1" file="vcffilter-test1.vcf"/> - </test> -</tests> - <help> - -You can specify the following options within the **Specify filtering expression** box in any combination:: - - -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter - -g, --genotype-filter specifies a filter to apply to the genotype fields of records - -s, --filter-sites filter entire records, not just alleles - -t, --tag-pass tag vcf records as positively filtered with this tag, print all records - -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records - -A, --append-filter append the existing filter tag, don't just replace it - -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag - -v, --invert inverts the filter, e.g. grep -v - -o, --or use logical OR instead of AND to combine filters - -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g) - -Filters are specified in the form {ID} {operator} {value}:: - - -f "DP > 10" # for info fields - -g "GT = 1|1" # for genotype fields - -f "CpG" # for 'flag' fields - -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. - -Operators can be any of: =, !, <, >, pipe, & - - -To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f):: - - -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20 - -r chrX # only output call on chromosome X - ------ - -Vcffilter @IS_PART_OF_VCFLIB@ -</help> - <expand macro="citations" /> -</tool> +<tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@.0"> + <description>filter VCF data in a variety of attributes</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="1.3">htslib</requirement> + <requirement type="package" version="0.2.6">tabix</requirement> + </expand> + <expand macro="stdio" /> + <command> + <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg --> + ln -s "${input1}" input1.vcf && + bgzip input1.vcf && + tabix -p vcf input1.vcf.gz && + vcffilter ${filterList} input1.vcf.gz > "${out_file1}" + </command> + + <inputs> + <param name="filterList" type="text" value="-f "DP > 10"" label="Specify filterting expression" help="See explanation of filtering options below"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + <param format="vcf" name="input1" type="data" label="VCF dataset to filter"/> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="filterList" value="-f "DP > 10""/> + <param name="input1" value="vcflib.vcf"/> + <output name="out_file1" file="vcffilter-test1.vcf"/> + </test> + </tests> + <help> +You can specify the following options within the **Specify filtering expression** box in any combination:: + + -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter + -g, --genotype-filter specifies a filter to apply to the genotype fields of records + -s, --filter-sites filter entire records, not just alleles + -t, --tag-pass tag vcf records as positively filtered with this tag, print all records + -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records + -A, --append-filter append the existing filter tag, don't just replace it + -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag + -v, --invert inverts the filter, e.g. grep -v + -o, --or use logical OR instead of AND to combine filters + -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g) + +Filters are specified in the form {ID} {operator} {value}:: + + -f "DP > 10" # for info fields + -g "GT = 1|1" # for genotype fields + -f "CpG" # for 'flag' fields + +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. + +Operators can be any of: =, !, <, >, pipe, & + + +To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f):: + + -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20 + -r chrX # only output call on chromosome X + +----- + +Vcffilter @IS_PART_OF_VCFLIB@ + </help> + <expand macro="citations" /> +</tool>