Mercurial > repos > iuc > bcftools_gtcheck

annotate bcftools_gtcheck.xml @ 0:92d82005d60a 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 06:55:28 -0400
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92d82005d60a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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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>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 #set $section = $sec_default
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16 #set $genotypes_vcf = None
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17 #if $section.genotypes:
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18 #if $section.genotypes.datatype.file_ext == 'vcf'
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19 #set $genotypes_vcf = 'genotypes.vcf.gz'
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20 bgzip -c "$section.genotypes" > $genotypes_vcf &&
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21 bcftools index $genotypes_vcf &&
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22 #elif $section.genotypes.datatype.file_ext == 'bcf'
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23 #set $genotypes_vcf = 'genotypes.bcf'
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24 ln -s "$ection.genotypes" $genotypes_vcf &&
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25 #if $section.genotypes.metadata.bcf_index:
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26 ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi &&
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27 #else
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28 bcftools index $genotypes_vcf &&
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29 #end if
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30 #end if
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31 #end if
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32
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33 bcftools @EXECUTABLE@
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34
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35 ## Default section
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36 #set $section = $sec_default
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37
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38 #if $genotypes_vcf:
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39 --genotypes $genotypes_vcf
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40 #end if
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41
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42 #if $section.genotypes:
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43 --genotypes "${section.genotypes}"
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44 #end if
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45
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46 ${section.all_sites}
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47
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48 #if $section.GTs_only:
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49 --GTs-only "${section.GTs_only}"
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50 #end if
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51
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52 ${section.homs_only}
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53
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54 #if $section.plot:
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55 --plot "${section.plot}"
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56 #end if
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57
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58 #if $section.query_sample:
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59 --query-sample "${section.query_sample}"
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60 #end if
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61
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62 #if $section.target_sample:
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63 --target-sample "${section.target_sample}"
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64 #end if
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65
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66 #set $section = $sec_restrict
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67 @REGIONS@
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68 @TARGETS@
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69
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70 ## Primary Input/Outputs
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71
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72 @INPUT_FILE@
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73 > "$output_file"
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74 ]]>
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75 </command>
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76 <inputs>
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77 <expand macro="macro_input" />
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78 <section name="sec_restrict" expanded="false" title="Restrict to">
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79 <expand macro="macro_regions" />
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80 <expand macro="macro_targets" />
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81 </section>
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82 <section name="sec_default" expanded="true" title="Default Options">
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83 <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True"
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84 help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/>
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85 <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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86 <param name="GTs_only" type="integer" label="Gts Only" default="99" optional="True" help="Use GTs, ignore PLs, using &lt;int&gt; for unseen genotypes" />
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87 <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" />
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88 <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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89 <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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90 <param name="plot" type="text" label="Plot" help="Prefix name for plot" />
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91 </section>
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92 </inputs>
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93 <outputs>
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94 <data name="output_file" format="tabular" />
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95 </outputs>
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96 <tests>
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97 <test>
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98 <param name="input_file" ftype="vcf" value="view.vcf" />
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99 <output name="output_file">
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100 <assert_contents>
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101 <has_text_matching expression="SM\t10328.0+\t80.68\t12\tNA00002\t0"/>
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102 <has_text_matching expression="CN\t1174\t14\t75.57\tNA00002\tNA00001"/>
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103 </assert_contents>
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104 </output>
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105 </test>
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106 </tests>
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107 <help><![CDATA[
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108 =====================================
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109 bcftools @EXECUTABLE@
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110 =====================================
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111
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112 Check sample identity. With no -g BCF given, multi-sample cross-check is performed.
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113
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114 @REGIONS_HELP@
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115 @TARGETS_HELP@
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116
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117 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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118
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119 @BCFTOOLS_WIKI@
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120
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121 ]]>
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122 </help>
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123 <expand macro="citations" />
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124 </tool>