Mercurial > repos > jjohnson > bcftools_plugin_vcf2sex

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sun, 26 Jun 2016 15:42:13 -0400
parents 255f41136132
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255f41136132 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_plugin_@PLUGIN_ID@" version="@VERSION@.0">
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3 <description>plugin Determine sample sex by checking genotypes in haploid regions</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">vcf2sex</token>
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6 <token name="@PLUGIN_ID@">vcf2sex</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
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17 bcftools plugin @EXECUTABLE@
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18
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19
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20 ## VCF input section
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21 #set $section = $sec_restrict
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22 @INCLUDE@
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23 @EXCLUDE@
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24 @REGIONS@
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25 @TARGETS@
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26
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27 ## Primary Input/Outputs
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28 @INPUT_FILE@
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29 ## Plugin section
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30 --
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31 #set $section = $sec_plugin
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32 #if $section.background:
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33 --background "${section.background}"
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34 #end if
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35 #if $section.guess:
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36 --guess $section.guess
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37 #end if
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38 #if $section.min_hets:
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39 --min-hets $section.min_hets
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40 #end if
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41 #if $section.nsites:
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42 --nsites $section.nsites
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43 #end if
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44 @PLOIDY_FILE@
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45 ${section.verbose}
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46 | tee "$output_file"
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47 ]]>
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48 </command>
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49 <inputs>
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50 <expand macro="macro_input" />
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51 <section name="sec_restrict" expanded="false" title="Restrict to">
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52 <expand macro="macro_regions" />
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53 <expand macro="macro_targets" />
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54 <expand macro="macro_include" />
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55 <expand macro="macro_exclude" />
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56 </section>
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57 <section name="sec_plugin" expanded="true" title="Plugin Options">
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58 <param name="background" type="text" value="" optional="true" label="background region">
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59 <help>
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60 Diploid region to determine normal hom/hets counts [X:60001-2699520]
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61 </help>
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62 <validator type="regex" message="">^(\w+:\d+-\d+)?$</validator>
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63 </param>
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64 <param name="guess" type="select" label="guess - determine ploidy by tag" optional="true"
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65 help="Determine ploidy by counting hom/hets (GT) or most likely genotypes (PL or GL)">
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66 <option value="GT">counting hom/hets (GT)</option>
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67 <option value="GL">most likely genotypes (GL)</option>
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68 <option value="PL">most likely genotypes (PL)</option>
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69 </param>
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70
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71 <param name="min_hets" type="float" value=".3" min="0." max="1." optional="true" label="min-hets - minimum fraction of hets in diploid regions [0.3]"
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72 help="(\-\-min-hets)"/>
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73 <param name="nsites" type="integer" value="10" min="0" optional="true" label="nsites - number of sites to check per region"
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74 help="(ignored with --guess) [10]"/>
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75
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76 <expand macro="macro_ploidy_file" />
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77 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Verbose"
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78 help="Print debugging information on plugin failure" />
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79
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80 </section>
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81 </inputs>
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82 <outputs>
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83 <data name="output_file" format="tabular"/>
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84 </outputs>
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85 <tests>
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86 <test>
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87 <param name="input_file" ftype="vcf" value="vcf2sex.vcf" />
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88 <param name="nsites" value="5" />
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89 <param name="output_type" value="v" />
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90 <output name="output_file">
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91 <assert_contents>
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92 <has_text text="MALE"/>
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93 </assert_contents>
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94 </output>
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95 </test>
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96 <test>
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97 <param name="input_file" ftype="vcf" value="vcf2sex.vcf" />
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98 <param name="guess" value="GT" />
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99 <param name="output_type" value="v" />
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100 <output name="output_file">
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101 <assert_contents>
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102 <has_text text="MALE"/>
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103 </assert_contents>
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104 </output>
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105 </test>
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106 <test>
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107 <param name="input_file" ftype="vcf" value="vcf2sex.vcf" />
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108 <param name="guess" value="GT" />
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109 <param name="nsites" value="5" />
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110 <param name="output_type" value="v" />
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111 <output name="output_file">
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112 <assert_contents>
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113 <has_text text="MALE"/>
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114 </assert_contents>
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115 </output>
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116 </test>
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117 </tests>
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118
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119 <help><![CDATA[
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120 =====================================
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121 bcftools @EXECUTABLE@ plugin
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122 =====================================
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123
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124 @REGIONS_HELP@
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125 @TARGETS_HELP@
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126 @EXPRESSIONS_HELP@
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127
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128 ]]></help>
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129 <expand macro="citations" />
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130 </tool>