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"planemo upload for repository https://github.com/phac-nml/gnali/ commit c3a811e4bb8ba8a718047c3324809175ad23291b"
author nml
date Thu, 29 Jul 2021 19:17:40 +0000
parents d1085589a5a7
children
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1 <tool id="gnali" name="gNALI" version="@VERSION@" python_template_version="3.7" profile="@PROFILE_VERSION@">
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2 <description>Get and filter nonessential, loss-of-function variants</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 gnali -i '$test_genes' -o output -d '$database_info.database'
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9 #if $database_info.predefined_filters != "None":
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10 --predefined_filters '$database_info.predefined_filters'
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11 #end if
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12 #if len($additional_filters) > 0:
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13 --additional_filters
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14 #for $filt in $additional_filters
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15 '$filt.filter'
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16 #end for
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17 #end if
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18 #if $vcf_output:
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19 '$vcf_output'
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20 #end if
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21 #if $pop_freqs:
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22 '$pop_freqs'
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23 #end if
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24 ]]></command>
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25 <inputs>
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26 <param type="data" name="test_genes" label="Test genes" format="txt" help="Specify a list of genes as HGNC symbols, separated by newline characters" />
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27 <param name="vcf_output" type="boolean" truevalue="--vcf" falsevalue="" optional="false" checked="false" label="VCF output" help="Generate vcf file for filtered variants" />
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28 <param name="pop_freqs" type="boolean" truevalue="--pop_freqs" falsevalue="" optional="false" checked="false" label="Population frequencies" help="Generate population frequency data for variants that passed filtering" />
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29 <conditional name="database_info">
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30 <param type="select" name="database" label="Database" format="txt" help="Database to query" >
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31 <option value="gnomadv2.1.1" selected="true">gnomADv2.1.1 (GRCh37/hg19)</option>
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32 <option value="gnomadv3.1.1">gnomADv3.1.1 (GRCh38/hg38)</option>
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33 </param>
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34 <when value="gnomadv2.1.1">
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35 <param name="predefined_filters" type="select" display="checkboxes" multiple="True" label="Predefined filters" help="Filter variants by selected filters">
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36 <option value="homozygous-controls">homozygous controls (controls_nhomalt>0)</option>
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37 <option value="heterozygous-controls">heterozygous controls (controls_nhomalt=0)</option>
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38 <option value="homozygous">homozygous (nhomalt>0)</option>
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39 </param>
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40 </when>
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41 <when value="gnomadv3.1.1">
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42 <param name="predefined_filters" type="select" display="checkboxes" multiple="True" label="Predefined filters" help="Filter variants by selected filters">
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43 <option value="homozygous">homozygous (nhomalt>0)</option>
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44 <option value="heterozygous">heterozygous (nhomalt=0)</option>
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45 </param>
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46 </when>
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47 </conditional>
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48 <repeat name="additional_filters" title="Additional filters" min="0" default="0" help="Additional filters (as expressions, ex. AC>10) to apply" >
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49 <param name="filter" type="text" optional="False" label="Filter">
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50 <sanitizer invalid_char="">
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51 <valid initial="string.ascii_letters,string.digits">
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52 <add value="&gt;" />
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53 <add value="&lt;" />
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54 <add value="=" />
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55 </valid>
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56 </sanitizer>
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57 </param>
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58 </repeat>
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59 </inputs>
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60 <outputs>
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61 <data name="basic_output" label="gNALI basic output on ${test_genes.element_identifier}" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Basic\).txt" />
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62 <data name="detailed_output" label="gNALI detailed output on ${test_genes.element_identifier}" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Detailed\).txt" />
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63 <data name="variants_vcf_output" label="gNALI variants vcf on ${test_genes.element_identifier}" format="vcf" from_work_dir="output/Nonessential_Gene_Variants.vcf" >
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64 <filter>vcf_output</filter>
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65 </data>
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66 </outputs>
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67 <tests>
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68 <test>
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69 <param name="test_genes" value="gnomadv2_input.txt"/>
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70 <param name="predefined_filters" value="homozygous-controls"/>
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71 <param name="pop_freqs" value="--pop_freqs"/>
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72 <param name="vcf_output" value="--vcf"/>
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73 <output name="basic_output"
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74 value="gnomadv2_results/Nonessential_Host_Genes_Basic.txt"
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75 ftype="txt"
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76 compare="diff">
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77 </output>
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78 <output name="detailed_output"
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79 value="gnomadv2_results/Nonessential_Host_Genes_Detailed.txt"
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80 ftype="txt"
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81 compare="diff">
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82 </output>
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83 <output name="variants_vcf_output"
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84 value="gnomadv2_results/Nonessential_Gene_Variants.vcf"
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85 ftype="vcf"
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86 compare="diff">
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87 </output>
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88 </test>
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89 <test>
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90 <param name="test_genes" value="gnomadv3_input.txt"/>
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91 <conditional name="database_info">
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92 <param name="database" value="gnomadv3.1.1"/>
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93 </conditional>
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94 <param name="predefined_filters" value="homozygous"/>
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95 <param name="pop_freqs" value="--pop_freqs"/>
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96 <param name="vcf_output" value="--vcf"/>
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97 <output name="basic_output"
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98 value="gnomadv3_results/Nonessential_Host_Genes_Basic.txt"
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99 ftype="txt"
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100 compare="diff">
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101 </output>
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102 <output name="detailed_output"
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103 value="gnomadv3_results/Nonessential_Host_Genes_Detailed.txt"
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104 ftype="txt"
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105 compare="diff">
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106 </output>
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107 <output name="variants_vcf_output"
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108 value="gnomadv3_results/Nonessential_Gene_Variants.vcf"
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109 ftype="vcf"
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110 compare="diff">
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111 </output>
2
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112 </test>
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113 </tests>
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114 <help><![CDATA[
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115
3
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116 Introduction
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117 ------------------
0
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118
3
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119 gNALI (gene nonessentiality and loss-of-function identifier) is a tool to find (high confidence)
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120 potential loss of function variants of genes.
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121
3
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122 NOTE: loss-of-function is influenced by the genome build. Not all variants available in gnomADv2.1.1 are
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123 available in gnomADv3.1.1 and vice versa.
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124
3
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125 Usage
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126 -----------
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127
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128 Your input file must be of format .csv, .txt, or tsv and should contain a list of genes
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129 (as HGNC symbols) to test, separated by newline characters.
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130 It should not contain any blank lines until the end of the list.
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131
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132
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133 **Population Frequencies**
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134
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135 When using the population frequencies feature:
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136
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137 Per population group:
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138
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139 * AC denotes allele count
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140
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141 * AN denotes allele number
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142
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143 * AF denotes allele frequency
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144
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145 ]]></help>
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146 <citations>
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147 <citation type="bibtex">
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148 @misc{GitHubgnali,
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149 author = {Xia, Liu},
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150 year = {2020},
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151 title = {gnali},
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152 publisher = {phac-nml},
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153 journal = {GitHub repository},
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154 url = {https://github.com/phac-nml/gnali/},
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155 }</citation>
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156 </citations>
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157 </tool>
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158