Mercurial > repos > iuc > bcftools_gtcheck

annotate bcftools_gtcheck.xml @ 22:7b4454382d39 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 784611c9caf2680d41414ca2880b93a69d719701
author iuc
date Sun, 18 Aug 2024 10:02:42 +0000
parents 91c1e57d5c7f
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1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Check sample identity</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">gtcheck</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools" />
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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_FILE@
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13 #set $section = $sec_restrict
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14 @PREPARE_TARGETS_FILE@
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15 @PREPARE_REGIONS_FILE@
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16 #set $section = $sec_default
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17 #set $genotypes_vcf = None
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18 #if $section.genotypes:
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19 #if $section.genotypes.is_of_type('vcf')
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20 #set $genotypes_vcf = 'genotypes.vcf.gz'
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21 bgzip -c '$section.genotypes' > $genotypes_vcf &&
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22 bcftools index $genotypes_vcf &&
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23 #elif $section.genotypes.is_of_type('bcf')
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24 #set $genotypes_vcf = 'genotypes.bcf'
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25 ln -s '$section.genotypes' $genotypes_vcf &&
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26 #if $section.genotypes.metadata.bcf_index:
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27 ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi &&
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28 #else
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29 bcftools index $genotypes_vcf &&
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30 #end if
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31 #end if
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32 #end if
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34 bcftools @EXECUTABLE@
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36 ## Default section
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37 #set $section = $sec_default
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39 #if $genotypes_vcf:
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40 --genotypes $genotypes_vcf
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41 #end if
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43 #if $section.genotypes:
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44 --genotypes '${section.genotypes}'
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45 #end if
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47 ${section.all_sites}
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49 ${section.homs_only}
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51 #if $section.plot:
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52 --plot '${section.plot}'
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53 #end if
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55 #if $section.query_sample:
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56 --query-sample '${section.query_sample}'
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57 #end if
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59 #if $section.target_sample:
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60 --target-sample '${section.target_sample}'
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61 #end if
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63 #set $section = $sec_restrict
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64 @REGIONS@
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65 @TARGETS@
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67 ## Primary Input/Outputs
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68
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69 @INPUT_FILE@
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70 > '$output_file'
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71 ]]>
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72 </command>
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73 <inputs>
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74 <expand macro="macro_input" />
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75 <section name="sec_restrict" expanded="false" title="Restrict to">
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76 <expand macro="macro_restrict" />
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77 <expand macro="macro_restrict" type="target" label_type="Target" />
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78 </section>
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79 <section name="sec_default" expanded="true" title="Default Options">
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80 <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True"
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81 help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/>
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82 <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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83 <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" />
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84 <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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85 <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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86 <param name="plot" type="text" label="Plot" help="Prefix name for plot" />
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87 </section>
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88 </inputs>
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89 <outputs>
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90 <data name="output_file" format="tabular" />
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91 </outputs>
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92 <tests>
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93 <test>
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94 <param name="input_file" ftype="vcf" value="view.vcf" />
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95 <output name="output_file">
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96 <assert_contents>
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97 <has_text_matching expression="DC\tNA00002\tNA00001\t6"/>
0
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98 </assert_contents>
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99 </output>
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100 </test>
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101 </tests>
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102 <help><![CDATA[
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103 =====================================
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104 bcftools @EXECUTABLE@
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105 =====================================
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106
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107 Check sample identity. With no -g BCF given, multi-sample cross-check is performed.
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108
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109 @REGIONS_HELP@
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110 @TARGETS_HELP@
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111
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112 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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113
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114 @BCFTOOLS_WIKI@
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115
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116 ]]>
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117 </help>
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118 <expand macro="citations" />
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119 </tool>