Mercurial > repos > iuc > bcftools_gtcheck

annotate bcftools_gtcheck.xml @ 9:64aa9ca7e702 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author iuc
date Wed, 05 Jun 2019 12:43:58 -0400
parents 2ba1da9c7f89
children 2f1d63010138
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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@+galaxy1">
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3 <description>Check sample identity</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">gtcheck</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_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 $genotypes_vcf = 'genotypes.bcf'
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25 ln -s '$ection.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 #if $section.GTs_only:
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50 --GTs-only '${section.GTs_only}'
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51 #end if
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53 ${section.homs_only}
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55 #if $section.plot:
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56 --plot '${section.plot}'
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57 #end if
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59 #if $section.query_sample:
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60 --query-sample '${section.query_sample}'
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61 #end if
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63 #if $section.target_sample:
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64 --target-sample '${section.target_sample}'
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65 #end if
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67 #set $section = $sec_restrict
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68 @REGIONS@
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69 @TARGETS@
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71 ## Primary Input/Outputs
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73 @INPUT_FILE@
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74 > '$output_file'
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75 ]]>
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76 </command>
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77 <inputs>
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78 <expand macro="macro_input" />
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79 <section name="sec_restrict" expanded="false" title="Restrict to">
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80 <expand macro="macro_restrict" />
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81 <expand macro="macro_restrict" type="target" label_type="Target" />
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82 </section>
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83 <section name="sec_default" expanded="true" title="Default Options">
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84 <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True"
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85 help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/>
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86 <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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87 <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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88 <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" />
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89 <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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90 <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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91 <param name="plot" type="text" label="Plot" help="Prefix name for plot" />
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92 </section>
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93 </inputs>
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94 <outputs>
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95 <data name="output_file" format="tabular" />
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96 </outputs>
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97 <tests>
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98 <test>
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99 <param name="input_file" ftype="vcf" value="view.vcf" />
5
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100 <param name="GTs_only" value="99" />
0
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101 <output name="output_file">
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102 <assert_contents>
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103 <has_text_matching expression="CN\t3\t10\t0\tNA00002\tNA00001"/>
0
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104 </assert_contents>
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105 </output>
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106 </test>
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107 </tests>
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108 <help><![CDATA[
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109 =====================================
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110 bcftools @EXECUTABLE@
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111 =====================================
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112
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113 Check sample identity. With no -g BCF given, multi-sample cross-check is performed.
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114
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115 @REGIONS_HELP@
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116 @TARGETS_HELP@
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117
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118 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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119
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120 @BCFTOOLS_WIKI@
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121
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122 ]]>
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123 </help>
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124 <expand macro="citations" />
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125 </tool>