Mercurial > repos > jjohnson > bcftools_query
diff bcftools_query.xml @ 0:bfea7fe50fd0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author | jjohnson |
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date | Sat, 25 Jun 2016 20:51:59 -0400 |
parents | |
children | 1610708580c3 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_query.xml Sat Jun 25 20:51:59 2016 -0400 @@ -0,0 +1,126 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0"> + <description>Extracts fields from VCF/BCF file and prints them in user-defined format</description> + <macros> + <token name="@EXECUTABLE@">query</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="aggressive"><![CDATA[ +@PREPARE_ENV@ +@PREPARE_INPUT_FILES@ +#set $section = $sec_restrict +@PREPARE_TARGETS_FILE@ + +bcftools @EXECUTABLE@ + +## Query section +#set $section = $sec_query + --format '${section.format}' + +${section.allow_undef_tags} + +${section.print_header} + +## Default section +#set $section = $sec_restrict +@INCLUDE@ +@EXCLUDE@ +@COLLAPSE@ +@REGIONS@ +@SAMPLES@ +@TARGETS@ + +## Primary Input/Outputs +--vcf-list @INPUT_LIST_FILE@ +> $output_file +]]> + </command> + <inputs> + <expand macro="macro_inputs" /> + <section name="sec_restrict" expanded="false" title="Restrict to"> + <expand macro="macro_collapse" /> + <expand macro="macro_samples" /> + <expand macro="macro_regions" /> + <expand macro="macro_targets" /> + <expand macro="macro_include" /> + <expand macro="macro_exclude" /> + </section> + <section name="sec_query" expanded="true" title="Query Options"> + <param name="format" type="text" value="" label="Format for Output"> + <help> + <![CDATA[ + Example: %CHROM\t%POS\t%REF\t%ALT{0}\n + ( NOTE TAB: '\t' and new line character: '\n' ) + ]]> + </help> + <sanitizer sanitize="False"/> + <validator type="empty_field" /> + </param> + <param name="tsv" type="boolean" truevalue="Y" falsevalue="N" checked="false" label="Output is tab-delimited" + help="Fields in your Format are separated by a TAB character: \t"/> + <param name="allow_undef_tags" type="boolean" truevalue="--allow-undef-tags" falsevalue="" label="Allow Undefined Tags" + help="Print "." for undefined tags" /> + <param name="print_header" type="boolean" truevalue="--print-header" falsevalue="" label="Print Header Line" /> + </section> + + </inputs> + <outputs> + <data name="output_file" format="txt"> + <change_format> + <when input="tsv" value="Y" format="tabular" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input_file" ftype="vcf" value="query.vcf" /> + <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" /> + <param name="tsv" value="true" /> + <output name="output_file" ftype="tabular" file="query.out" /> + </test> + </tests> + <help><![CDATA[ +===================================== + bcftools @EXECUTABLE@ +===================================== + +Extracts fields from VCF/BCF file and prints them in user-defined format + + Format: + + :: + + ``%CHROM`` The CHROM column (similarly also other columns: POS, ID, REF, ALT, QUAL, FILTER) + ``%INFO/TAG`` Any tag in the INFO column + ``%TYPE`` Variant type (REF, SNP, MNP, INDEL, OTHER) + ``%MASK`` Indicates presence of the site in other files (with multiple files) + ``%TAG{INT}`` Curly brackets to subscript vectors (0-based) + ``%FIRST_ALT`` Alias for %ALT{0} + ``[]`` The brackets loop over all samples + ``%GT`` Genotype (e.g. 0/1) + ``%TGT`` Translated genotype (e.g. C/A) + ``%IUPACGT`` Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A) + ``%LINE`` Prints the whole line + ``%SAMPLE`` Sample name + + Examples: + + :: + + ``bcftools query -f '%CHROM %POS %REF %ALT{0}\n' file.vcf.gz`` + ``bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz`` + +@COLLAPSE_HELP@ +@REGIONS_HELP@ +@TARGETS_HELP@ +@EXPRESSIONS_HELP@ + +@BCFTOOLS_MANPAGE@#@EXECUTABLE@ + +@BCFTOOLS_WIKI@ +]]> + </help> + <expand macro="citations" /> +</tool>