Mercurial > repos > devteam > vcffilter
changeset 4:6b935ab36d7b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
author | iuc |
---|---|
date | Mon, 26 Mar 2018 10:21:29 -0400 |
parents | 952059348a30 |
children | de885f4afb7f |
files | vcffilter.xml |
diffstat | 1 files changed, 55 insertions(+), 26 deletions(-) [+] |
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--- a/vcffilter.xml Fri Sep 30 10:35:47 2016 -0400 +++ b/vcffilter.xml Mon Mar 26 10:21:29 2018 -0400 @@ -1,44 +1,72 @@ -<tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@.0"> +<tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy1"> <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="1.7">htslib</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> - + <command><![CDATA[ +ln -s '$input1' input1.vcf && +bgzip input1.vcf && +tabix -p vcf input1.vcf.gz && +vcffilter +#for $filter_el in $filter_repeat: + $filter_el.filter_type '$filter_el.filter_value' +#end for +$filter_sites +$tag_pass +$tag_fail +$append_filter +$allele_tag +$invert +$or +#if str($region): + --region '$region' +#end if +input1.vcf.gz +> '${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 name="input1" type="data" format="vcf" label="VCF dataset to filter"/> + <repeat name="filter_repeat" title="Add filters"> + <param name="filter_type" type="select" label="Select the filter type"> + <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"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </repeat> + <param name="filter_sites" argument="--filter-sites" type="boolean" truevalue="--filter-sites" falsevalue="" label="Filter entire records, not just alleles"/> + <param name="tag_pass" argument="--tag-pass" type="boolean" truevalue="--tag-pass" falsevalue="" label="Tag vcf records as positively filtered with this tag, print all records"/> + <param name="tag_fail" argument="--tag-fail" type="boolean" truevalue="--tag-fail" falsevalue="" label="Tag vcf records as negatively filtered with this tag, print all records"/> + <param name="append_filter" argument="--append-filter" type="boolean" truevalue="--append-filter" falsevalue="" label="Append the existing filter tag, don't just replace it"/> + <param name="allele_tag" argument="--allele-tag" type="boolean" truevalue="--allele-tag" falsevalue="" label="Apply --tag-pass on a per-allele basis, adds or sets the corresponding INFO field tag"/> + <param argument="--invert" type="boolean" truevalue="--invert" falsevalue="" label="Inverts the filter, e.g. grep -v"/> + <param argument="--or" type="boolean" truevalue="--or" falsevalue="" label="Use logical OR instead of AND to combine filters"/> + <param argument="--region" type="text" label="Specify a region on which to target the filtering" help="Regions should be specified as chr:start-end, e.g X:1000-2000"/> </inputs> <outputs> - <data format="vcf" name="out_file1" /> + <data name="out_file1" format="vcf" /> </outputs> <tests> <test> - <param name="filterList" value="-f "DP > 10""/> + <param name="filter_repeat_0|filter_type" value="-f"/> + <param name="filter_repeat_0|filter_value" value="DP > 10"/> <param name="input1" value="vcflib.vcf"/> <output name="out_file1" file="vcffilter-test1.vcf"/> </test> </tests> - <help> + <help><![CDATA[ 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 @@ -60,8 +88,9 @@ 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, & +Operators can be any of:: + =, !, <, >, |, & To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f):: @@ -71,6 +100,6 @@ ----- Vcffilter @IS_PART_OF_VCFLIB@ - </help> + ]]></help> <expand macro="citations" /> </tool>