Mercurial > repos > jjohnson > bcftools_query

annotate bcftools_query.xml @ 0:bfea7fe50fd0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sat, 25 Jun 2016 20:51:59 -0400
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children 1610708580c3
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bfea7fe50fd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
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3 <description>Extracts fields from VCF/BCF file and prints them in user-defined format</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">query</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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10 <command detect_errors="aggressive"><![CDATA[
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11 @PREPARE_ENV@
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12 @PREPARE_INPUT_FILES@
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13 #set $section = $sec_restrict
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14 @PREPARE_TARGETS_FILE@
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15
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16 bcftools @EXECUTABLE@
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17
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18 ## Query section
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19 #set $section = $sec_query
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20 --format '${section.format}'
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21
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22 ${section.allow_undef_tags}
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23
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24 ${section.print_header}
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25
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26 ## Default section
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27 #set $section = $sec_restrict
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28 @INCLUDE@
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29 @EXCLUDE@
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30 @COLLAPSE@
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31 @REGIONS@
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32 @SAMPLES@
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33 @TARGETS@
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34
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35 ## Primary Input/Outputs
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36 --vcf-list @INPUT_LIST_FILE@
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37 > $output_file
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38 ]]>
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39 </command>
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40 <inputs>
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41 <expand macro="macro_inputs" />
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42 <section name="sec_restrict" expanded="false" title="Restrict to">
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43 <expand macro="macro_collapse" />
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44 <expand macro="macro_samples" />
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45 <expand macro="macro_regions" />
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46 <expand macro="macro_targets" />
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47 <expand macro="macro_include" />
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48 <expand macro="macro_exclude" />
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49 </section>
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50 <section name="sec_query" expanded="true" title="Query Options">
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51 <param name="format" type="text" value="" label="Format for Output">
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52 <help>
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53 <![CDATA[
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54 Example: %CHROM\t%POS\t%REF\t%ALT{0}\n
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55 ( NOTE TAB: '\t' and new line character: '\n' )
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56 ]]>
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57 </help>
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58 <sanitizer sanitize="False"/>
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59 <validator type="empty_field" />
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60 </param>
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61 <param name="tsv" type="boolean" truevalue="Y" falsevalue="N" checked="false" label="Output is tab-delimited"
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62 help="Fields in your Format are separated by a TAB character: \t"/>
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63 <param name="allow_undef_tags" type="boolean" truevalue="--allow-undef-tags" falsevalue="" label="Allow Undefined Tags"
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64 help="Print &quot;.&quot; for undefined tags" />
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65 <param name="print_header" type="boolean" truevalue="--print-header" falsevalue="" label="Print Header Line" />
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66 </section>
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67
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68 </inputs>
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69 <outputs>
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70 <data name="output_file" format="txt">
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71 <change_format>
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72 <when input="tsv" value="Y" format="tabular" />
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73 </change_format>
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74 </data>
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75 </outputs>
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76 <tests>
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77 <test>
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78 <param name="input_file" ftype="vcf" value="query.vcf" />
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79 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" />
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80 <param name="tsv" value="true" />
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81 <output name="output_file" ftype="tabular" file="query.out" />
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82 </test>
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83 </tests>
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84 <help><![CDATA[
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85 =====================================
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86 bcftools @EXECUTABLE@
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87 =====================================
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88
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89 Extracts fields from VCF/BCF file and prints them in user-defined format
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90
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91 Format:
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92
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93 ::
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94
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95 ``%CHROM`` The CHROM column (similarly also other columns: POS, ID, REF, ALT, QUAL, FILTER)
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96 ``%INFO/TAG`` Any tag in the INFO column
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97 ``%TYPE`` Variant type (REF, SNP, MNP, INDEL, OTHER)
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98 ``%MASK`` Indicates presence of the site in other files (with multiple files)
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99 ``%TAG{INT}`` Curly brackets to subscript vectors (0-based)
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100 ``%FIRST_ALT`` Alias for %ALT{0}
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101 ``[]`` The brackets loop over all samples
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102 ``%GT`` Genotype (e.g. 0/1)
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103 ``%TGT`` Translated genotype (e.g. C/A)
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104 ``%IUPACGT`` Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A)
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105 ``%LINE`` Prints the whole line
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106 ``%SAMPLE`` Sample name
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107
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108 Examples:
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109
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110 ::
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111
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112 ``bcftools query -f '%CHROM %POS %REF %ALT{0}\n' file.vcf.gz``
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113 ``bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz``
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114
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115 @COLLAPSE_HELP@
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116 @REGIONS_HELP@
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117 @TARGETS_HELP@
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118 @EXPRESSIONS_HELP@
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119
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120 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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121
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122 @BCFTOOLS_WIKI@
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123 ]]>
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124 </help>
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125 <expand macro="citations" />
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126 </tool>