Mercurial > repos > iuc > bcftools_plugin_mendelian

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:50:43 +0000
parents 2776dd881da8
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1 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>plugin Count Mendelian consistent / inconsistent genotypes</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">mendelian2</token>
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5 <token name="@PLUGIN_ID@">mendelian</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="bio_tools" />
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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_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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17 bcftools plugin @EXECUTABLE@
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19 ## VCF input section
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20 #set $section = $sec_restrict
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21 @INCLUDE@
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22 @EXCLUDE@
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23 @REGIONS@
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24 @TARGETS@
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26 @OUTPUT_TYPE@
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28 ## Primary Input/Outputs
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29 @INPUT_FILE@
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31 ## Plugin section
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32 #set $section = $sec_plugin
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33 #if $section.trios.trios_src == 'trio':
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34 --pfm '${section.trios.num_x}:${section.trios.child},${section.trios.mother},${section.trios.father}'
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35 #elif $section.trios.trios_src == 'trio_file':
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36 --ped '$section.trios.trio_file'
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37 #end if
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38 #set $modes = "".join(str($section.mode).split(','))
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39 -m $modes
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40 2> tmp_stderr
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41 > '$output_file'
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42 && cat tmp_stderr
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43 ]]>
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44 </command>
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45 <inputs>
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46 <expand macro="macro_input" />
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47 <section name="sec_restrict" expanded="false" title="Restrict to">
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48 <expand macro="macro_region_restrict" />
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49 <expand macro="macro_target_restrict" />
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50 <expand macro="macro_include" />
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51 <expand macro="macro_exclude" />
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52 </section>
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53 <section name="sec_plugin" expanded="true" title="Plugin Options">
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54 <!-- trios -->
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55 <conditional name="trios">
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56 <param name="trios_src" type="select" label="Sample relationship">
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57 <option value="trio">trio - mother,father,child (--pfm)</option>
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58 <option value="trio_file">trios file - specify 1 or more trios in PED format (--ped)</option>
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59 </param>
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60 <when value="trio">
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61 <param name="mother" type="text" value="" label="Mother sample name (as it appears in the input)"/>
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62 <param name="father" type="text" value="" label="Father sample name (as it appears in the input)"/>
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63 <param name="child" type="text" value="" label="Child sample name (as it appears in the input)"/>
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64 <param name="num_x" type="boolean" truevalue="1X" falsevalue="2X" label="Male child?" help="This information is used to judge inheritance patterns of X-chromosomal mutations correctly."/>
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65 </when>
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66 <when value="trio_file">
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67 <param name="trio_file" type="data" format="tabular" label="Sample information in PED format" help="This input dataset can describe one or several family trios. See the tool help below for more information on PED format." />
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68 </when>
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69 </conditional>
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70 <param name="mode" type="select" multiple="true" optional="false" label="Output mode" help="Output mode. Multiple modes can be combined and the drop modes take precedence.">
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71 <option value="a" selected="true">add INFO -> MERR annotation with the number of inconsistent trios (a)</option>
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72 <option value="d">delete (i.e., set to "./.") genotypes in inconsistent trios (d)</option>
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73 <option value="e">output sites with at least one erroneous trio (e)</option>
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74 <option value="E">drop sites with at least one erroneous trio (E)</option>
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75 <option value="g">output sites with at least one good (i.e. with non-missing and consistent genotypes) trio (g)</option>
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76 <option value="m">output sites with missing genotypes in at least one trio (m)</option>
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77 <option value="M">drop sites with missing genotypes in at least one trio (M)</option>
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78 <option value="S">drop sites skipped for various reasons when collecting stats (S)</option>
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79 </param>
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80 </section>
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81 <expand macro="macro_select_output_type" />
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82 </inputs>
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83 <outputs>
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84 <expand macro="macro_vcf_output" />
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85 </outputs>
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86 <tests>
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87 <test>
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88 <!-- This is just a test on a random file, should have a real test case -->
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89 <param name="input_file" ftype="vcf" value="convert.vcf" />
25
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90 <section name="sec_plugin">
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91 <conditional name="trios">
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92 <param name="trios_src" value="trio" />
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93 <param name="mother" value="NA00001" />
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94 <param name="father" value="NA00002" />
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95 <param name="child" value="NA00006" />
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96 </conditional>
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97 <param name="mode" value="d" />
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98 </section>
0
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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>
5
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102 <has_text_matching expression="X\t2698769\t.\tAAG\tA\t999\t.\t.\tGT:PL:GP\t./."/>
0
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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 <!-- This is just a test on a random file, should have a real test case -->
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108 <param name="input_file" ftype="vcf" value="convert.vcf" />
25
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109 <section name="sec_plugin">
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110 <conditional name="trios">
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111 <param name="trios_src" value="trio" />
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112 <param name="mother" value="NA00001" />
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113 <param name="father" value="NA00002" />
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114 <param name="child" value="NA00006" />
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115 </conditional>
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116 <param name="mode" value="e" />
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117 </section>
0
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118 <param name="output_type" value="v" />
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119 <output name="output_file">
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120 <assert_contents>
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121 <not_has_text text="2698758" />
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122 <has_text text="2698769" />
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123 </assert_contents>
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124 </output>
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125 </test>
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126 </tests>
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127
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128 <help><![CDATA[
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129 =====================================
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130 bcftools @EXECUTABLE@ plugin
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131 =====================================
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132
25
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133
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134 Describing sample relationships (family trios) in PED format
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135 ------------------------------------------------------------
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136
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137 A PED file is simply a tabular text file (columns can be separated by either
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138 spaces or TABs, but not a mixture of the two within the same file) with the
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139 header::
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140
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141 #family_id name paternal_id maternal_id sex
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142
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143 and optional additional columns. The actual column names in the header are not
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144 fixed, but there have to be at least six columns that are interpreted as
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145 detailed next.
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146
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147 Subsequent lines describe one sample from the VCF input dataset each, where
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148
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149 - *family_id* is an alphanumeric identifier of a family
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150
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151 This column has to be present, but is ignored by this plugin
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152
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153 - *name* is the identifier of the sample described by the line
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154
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155 - *paternal_id* is the identifier of the sample's father
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156
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157 - *maternal_id* is the identifier of the sample's mother
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158
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159 - *sex* is a numeric code (1=male, 2=female) for the sample's sex
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160
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161 An example minimal PED file describing a single family-trio with a female child could look like this::
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162
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163 #family_id name paternal_id maternal_id sex
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164 0 NA00001 0 0 1
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165 0 NA00002 0 0 2
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166 0 NA00003 NA00001 NA00002 2
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167
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168 where 0 is used as a placeholder for the paternal_id/maternal_id values in the records of the father and mother.
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169
0
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170 @REGIONS_HELP@
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171 @TARGETS_HELP@
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172 @EXPRESSIONS_HELP@
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173
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174 ]]></help>
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175 <expand macro="citations" />
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176 </tool>