Mercurial > repos > iuc > bcftools_gtcheck

annotate bcftools_gtcheck.xml @ 13:39810174657a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
author iuc
date Thu, 14 Oct 2021 10:00:26 +0000
parents fd1030bc93d9
children 64778f8899cc
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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="@TOOL_VERSION@">
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3 <description>Check sample identity</description>
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4 <expand macro="bio_tools" />
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5 <macros>
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6 <token name="@EXECUTABLE@">gtcheck</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="version_command" />
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11 <command detect_errors="aggressive"><![CDATA[
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12 @PREPARE_ENV@
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13 @PREPARE_INPUT_FILE@
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14 #set $section = $sec_restrict
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15 @PREPARE_TARGETS_FILE@
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16 @PREPARE_REGIONS_FILE@
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17 #set $section = $sec_default
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18 #set $genotypes_vcf = None
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19 #if $section.genotypes:
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20 #if $section.genotypes.is_of_type('vcf')
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21 #set $genotypes_vcf = 'genotypes.vcf.gz'
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22 bgzip -c '$section.genotypes' > $genotypes_vcf &&
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23 bcftools index $genotypes_vcf &&
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24 #elif $section.genotypes.is_of_type('bcf')
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25 #set $genotypes_vcf = 'genotypes.bcf'
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26 ln -s '$ection.genotypes' $genotypes_vcf &&
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27 #if $section.genotypes.metadata.bcf_index:
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28 ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi &&
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29 #else
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30 bcftools index $genotypes_vcf &&
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31 #end if
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32 #end if
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33 #end if
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35 bcftools @EXECUTABLE@
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37 ## Default section
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38 #set $section = $sec_default
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40 #if $genotypes_vcf:
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41 --genotypes $genotypes_vcf
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42 #end if
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44 #if $section.genotypes:
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45 --genotypes '${section.genotypes}'
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46 #end if
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48 ${section.all_sites}
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50 #if $section.GTs_only:
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51 --GTs-only '${section.GTs_only}'
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52 #end if
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54 ${section.homs_only}
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56 #if $section.plot:
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57 --plot '${section.plot}'
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58 #end if
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60 #if $section.query_sample:
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61 --query-sample '${section.query_sample}'
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62 #end if
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64 #if $section.target_sample:
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65 --target-sample '${section.target_sample}'
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66 #end if
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68 #set $section = $sec_restrict
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69 @REGIONS@
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70 @TARGETS@
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72 ## Primary Input/Outputs
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74 @INPUT_FILE@
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75 > '$output_file'
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76 ]]>
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77 </command>
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78 <inputs>
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79 <expand macro="macro_input" />
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80 <section name="sec_restrict" expanded="false" title="Restrict to">
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81 <expand macro="macro_restrict" />
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82 <expand macro="macro_restrict" type="target" label_type="Target" />
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83 </section>
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84 <section name="sec_default" expanded="true" title="Default Options">
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85 <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True"
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86 help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/>
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87 <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" />
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88 <param name="GTs_only" type="integer" label="Gts Only" value="99" optional="True" help="Use GTs, ignore PLs, using &lt;int&gt; for unseen genotypes" />
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89 <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" />
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90 <param name="homs_only" type="boolean" truevalue="--homs-only" falsevalue="" label="Homs Only" help="Homozygous genotypes only (useful for low coverage data)" />
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91 <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query sample (by default the first sample is checked)" />
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92 <param name="plot" type="text" label="Plot" help="Prefix name for plot" />
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93 </section>
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94 </inputs>
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95 <outputs>
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96 <data name="output_file" format="tabular" />
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97 </outputs>
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98 <tests>
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99 <test>
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100 <param name="input_file" ftype="vcf" value="view.vcf" />
5
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101 <param name="GTs_only" value="99" />
0
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102 <output name="output_file">
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103 <assert_contents>
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104 <has_text_matching expression="CN\t3\t10\t0\tNA00002\tNA00001"/>
0
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105 </assert_contents>
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106 </output>
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107 </test>
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108 </tests>
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109 <help><![CDATA[
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110 =====================================
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111 bcftools @EXECUTABLE@
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112 =====================================
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113
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114 Check sample identity. With no -g BCF given, multi-sample cross-check is performed.
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115
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116 @REGIONS_HELP@
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117 @TARGETS_HELP@
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118
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119 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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120
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121 @BCFTOOLS_WIKI@
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122
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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>