Mercurial > repos > iuc > bcftools_plugin_mendelian

annotate bcftools_plugin_mendelian.xml @ 7:3ff5654b4e7d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
author iuc
date Thu, 21 Feb 2019 16:01:33 -0500
parents f0747a281247
children 8c5c747e2bb4
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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="@TOOL_VERSION@">
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3 <description>plugin Count Mendelian consistent / inconsistent genotypes</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">mendelian</token>
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6 <token name="@PLUGIN_ID@">mendelian</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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18 bcftools plugin @EXECUTABLE@
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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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27 @OUTPUT_TYPE@
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28
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29 ## Primary Input/Outputs
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30 @INPUT_FILE@
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31
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32 ## Plugin section
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33 #set $section = $sec_plugin
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34 #if $section.trios.trios_src == 'trio':
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35 --trio "${section.trios.mother},${section.trios.father},${section.trios.child}"
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36 #elif $section.trios.trios_src == 'trio_file':
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37 --trio-file "$section.trios.trio_file"
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38 #end if
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39 #if $section.mode:
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40 #set $modes = str($section.mode).split(',')
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41 #if 'count' in $modes:
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42 --count
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43 #end if
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44 #if 'delete' in $modes:
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45 --delete
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46 #end if
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47 #if '+' in $modes:
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48 --list '+'
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49 #end if
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50 #if 'x' in $modes:
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51 --list x
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52 #end if
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53 #end if
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54 2> tmp_stderr
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55 > '$output_file'
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56 && cat tmp_stderr
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57 ]]>
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58 </command>
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59 <inputs>
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60 <expand macro="macro_input" />
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61 <section name="sec_restrict" expanded="false" title="Restrict to">
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62 <expand macro="macro_regions" />
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63 <expand macro="macro_targets" />
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64 <expand macro="macro_include" />
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65 <expand macro="macro_exclude" />
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66 </section>
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67 <section name="sec_plugin" expanded="true" title="Plugin Options">
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68 <!-- trios -->
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69 <conditional name="trios">
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70 <param name="trios_src" type="select" label="Sample relationship">
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71 <option value="trio">trio - mother,father,child</option>
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72 <option value="trio_file">trios file</option>
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73 </param>
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74 <when value="trio">
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75 <param name="mother" type="text" value="" label="name of mother"/>
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76 <param name="father" type="text" value="" label="name of father"/>
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77 <param name="child" type="text" value="" label="name of child"/>
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78 </when>
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79 <when value="trio_file">
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80 <param name="trio_file" type="data" format="txt" label="Trio File" help="List of trios, one per line" />
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81 </when>
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82 </conditional>
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83 <param name="mode" type="select" label="Action" multiple="true" min="1">
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84 <option value="count">count the number of consistent sites</option>
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85 <option value="delete">delete inconsistent genotypes (set to './.')</option>
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86 <option value="+">list consistent sites (+)</option>
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87 <option value="x">list inconsistent sites (x)</option>
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88 </param>
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89 </section>
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90 <expand macro="macro_select_output_type" />
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91 </inputs>
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92 <outputs>
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93 <expand macro="macro_vcf_output" />
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94 </outputs>
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95 <tests>
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96 <test>
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97 <!-- This is just a test on a random file, should have a real test case -->
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98 <param name="input_file" ftype="vcf" value="convert.vcf" />
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99 <param name="trios_src" value="trio" />
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100 <param name="mother" value="NA00001" />
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101 <param name="father" value="NA00002" />
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102 <param name="child" value="NA00006" />
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103 <param name="mode" value="delete" />
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104 <param name="output_type" value="v" />
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105 <output name="output_file">
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106 <assert_contents>
5
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107 <has_text_matching expression="X\t2698769\t.\tAAG\tA\t999\t.\t.\tGT:PL:GP\t./."/>
0
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108 </assert_contents>
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109 </output>
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110 </test>
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111 <test>
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112 <!-- This is just a test on a random file, should have a real test case -->
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113 <param name="input_file" ftype="vcf" value="convert.vcf" />
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114 <param name="trios_src" value="trio" />
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115 <param name="mother" value="NA00001" />
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116 <param name="father" value="NA00002" />
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117 <param name="child" value="NA00006" />
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118 <param name="mode" value="x" />
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119 <param name="output_type" value="v" />
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120 <output name="output_file">
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121 <assert_contents>
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122 <not_has_text text="2698758" />
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123 <has_text text="2698769" />
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124 </assert_contents>
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125 </output>
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126 </test>
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127
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128 </tests>
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129
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130 <help><![CDATA[
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131 =====================================
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132 bcftools @EXECUTABLE@ plugin
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133 =====================================
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134
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135 @REGIONS_HELP@
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136 @TARGETS_HELP@
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137 @EXPRESSIONS_HELP@
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138
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139 ]]></help>
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140 <expand macro="citations" />
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141 </tool>