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comparison bcftools_query.xml @ 0:38feefda21ce draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 06:59:10 -0400
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children 19e871cd19ab
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1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
3 <description>Extracts fields from VCF/BCF file and prints them in user-defined format</description>
4 <macros>
5 <token name="@EXECUTABLE@">query</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <expand macro="version_command" />
10 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@
12 @PREPARE_INPUT_FILES@
13 #set $section = $sec_restrict
14 @PREPARE_TARGETS_FILE@
15
16 bcftools @EXECUTABLE@
17
18 ## Query section
19 #set $section = $sec_query
20 --format '${section.format}'
21
22 ${section.allow_undef_tags}
23
24 ${section.print_header}
25
26 ## Default section
27 #set $section = $sec_restrict
28 @INCLUDE@
29 @EXCLUDE@
30 @COLLAPSE@
31 @REGIONS@
32 @SAMPLES@
33 @TARGETS@
34
35 ## Primary Input/Outputs
36 --vcf-list @INPUT_LIST_FILE@
37 > $output_file
38 ]]>
39 </command>
40 <inputs>
41 <expand macro="macro_inputs" />
42 <section name="sec_restrict" expanded="false" title="Restrict to">
43 <expand macro="macro_collapse" />
44 <expand macro="macro_samples" />
45 <expand macro="macro_regions" />
46 <expand macro="macro_targets" />
47 <expand macro="macro_include" />
48 <expand macro="macro_exclude" />
49 </section>
50 <section name="sec_query" expanded="true" title="Query Options">
51 <param name="format" type="text" value="" label="Format for Output">
52 <help>
53 <![CDATA[
54 Example: %CHROM\t%POS\t%REF\t%ALT{0}\n
55 ( NOTE TAB: '\t' and new line character: '\n' )
56 ]]>
57 </help>
58 <sanitizer sanitize="False"/>
59 <validator type="empty_field" />
60 </param>
61 <param name="tsv" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Output is tab-delimited"
62 help="Fields in your Format are separated by a TAB character: \t"/>
63 <param name="allow_undef_tags" type="boolean" truevalue="--allow-undef-tags" falsevalue="" label="Allow Undefined Tags"
64 help="Print &quot;.&quot; for undefined tags" />
65 <param name="print_header" type="boolean" truevalue="--print-header" falsevalue="" label="Print Header Line" />
66 </section>
67
68 </inputs>
69 <outputs>
70 <data name="output_file" format="txt">
71 <change_format>
72 <when input="tsv" value="True" format="tabular" />
73 </change_format>
74 </data>
75 </outputs>
76 <tests>
77 <test>
78 <param name="input_files" ftype="vcf" value="query.vcf" />
79 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" />
80 <param name="tsv" value="True" />
81 <output name="output_file" file="query.out" />
82 </test>
83 </tests>
84 <help><![CDATA[
85 =====================================
86 bcftools @EXECUTABLE@
87 =====================================
88
89 Extracts fields from VCF/BCF file and prints them in user-defined format
90
91 Format:
92
93 ::
94
95 ``%CHROM`` The CHROM column (similarly also other columns: POS, ID, REF, ALT, QUAL, FILTER)
96 ``%INFO/TAG`` Any tag in the INFO column
97 ``%TYPE`` Variant type (REF, SNP, MNP, INDEL, OTHER)
98 ``%MASK`` Indicates presence of the site in other files (with multiple files)
99 ``%TAG{INT}`` Curly brackets to subscript vectors (0-based)
100 ``%FIRST_ALT`` Alias for %ALT{0}
101 ``[]`` The brackets loop over all samples
102 ``%GT`` Genotype (e.g. 0/1)
103 ``%TGT`` Translated genotype (e.g. C/A)
104 ``%IUPACGT`` Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A)
105 ``%LINE`` Prints the whole line
106 ``%SAMPLE`` Sample name
107
108 Examples:
109
110 ::
111
112 ``bcftools query -f '%CHROM %POS %REF %ALT{0}\n' file.vcf.gz``
113 ``bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz``
114
115 @COLLAPSE_HELP@
116 @REGIONS_HELP@
117 @TARGETS_HELP@
118 @EXPRESSIONS_HELP@
119
120 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
121
122 @BCFTOOLS_WIKI@
123 ]]>
124 </help>
125 <expand macro="citations" />
126 </tool>