Mercurial > repos > iuc > tb_variant_filter

annotate tb_variant_filter.xml @ 0:3b1e7c170b10 draft

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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
author iuc
date Thu, 10 Oct 2019 17:59:02 -0400
parents
children eee2da03d1f5
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0
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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1 <tool id="tb_variant_filter" name="TB Variant Filter" version="@TOOL_VERSION@+galaxy0" profile="16.04">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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2 <description>M. tuberculosis H37Rv VCF filter</description>
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.1.3</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">tb_variant_filter</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 tb_variant_filter
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11 #if "region_filter" in str($filters).split(',')
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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12 #if str($filter_options.show_filter_options) == "yes":
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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13 --region_filter $filter_options.region_filter
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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14 #else
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15 --region_filter pe_ppe,uvp
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16 #end if
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17 #end if
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18 #if "close_to_indel_filter" in str($filters).split(',')
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19 --close_to_indel_filter
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20 #if str($filter_options.show_filter_options) == "yes":
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21 --indel_window_size $filter_options.indel_window_size
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22 #end if
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23 #end if
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24 #if "min_percentage_alt_filter" in str($filters).split(',')
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25 --min_percentage_alt_filter
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26 #if str($filter_options.show_filter_options) == "yes":
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27 --min_percentage_alt $filter_options.min_percentage_alt
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28 #end if
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29 #end if
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30 #if "min_depth_filter" in str($filters).split(',')
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31 --min_depth_filter
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32 #if str($filter_options.show_filter_options) == "yes":
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33 --min_depth $filter_options.min_depth
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34 #end if
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35 #end if
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36 #if "snv_only_filter" in str($filters).split(','):
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37 --snv_only_filter
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38 #end if
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39 '$input1' '$output1'
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40 ]]></command>
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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41 <inputs>
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42 <param type="data" name="input1" label="VCF file to be filter" format="vcf"/>
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43
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44 <param type="select" name="filters" multiple="true" label="Filters to apply">
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45 <option value="region_filter" selected="true">Filter out variants by regions</option>
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46 <option value="close_to_indel_filter">Filter variants close to indels</option>
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47 <option value="min_percentage_alt_filter">Filter variants by percentage alt allele</option>
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48 <option value="min_depth_filter">Filter sites by read alignment depth</option>
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49 <option value="snv_only_filter">Only accept SNVs</option>
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50 </param>
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51
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52 <conditional name="filter_options">
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53 <param type="select" name="show_filter_options" label="Show options for the filters">
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54 <option value="yes">Yes</option>
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55 <option value="no" selected="true">No</option>
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56 </param>
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57 <when value="yes">
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58 <param argument="--region_filter" type="select" multiple="true" label="Region filters to enable">
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59 <!-- if these are changed the code above needs to change to keep the defaults in line with those that are default here -->
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60 <option value="pe_ppe" selected="true">PE/PPE</option>
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61 <option value="tbprofiler">TBProfiler antibiotic resistant genes</option>
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62 <option value="mtbseq">MTBseq antibiotic resistant genes</option>
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63 <option value="uvp" selected="true">UVP repeat / insertion sequence sites</option>
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64 </param>
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65 <param argument="--indel_window_size" type="integer" value="5" label="Window to mask around indels"/>
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66 <param argument="--min_percentage_alt" type="float" value="90"
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67 label="Minimum alternate allele percentage to accept"/>
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68 <param argument="--min_depth" type="integer" value="30" label="Minimum read depth (coverage)"/>
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69 </when>
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70 <when value="no"></when>
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71
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72 </conditional>
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73 </inputs>
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74 <outputs>
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75 <data name="output1" format="vcf"/>
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76 </outputs>
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77 <tests>
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78 <test>
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79 <param name="input1" value="test_input1.vcf" ftype="vcf" />
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80 <param name="filters" value="region_filter" />
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81 <conditional name="filter_options">
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82 <param name="show_filter_options" value="yes" />
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83 <param name="region_filter" value="pe_ppe,tbprofiler,uvp" />
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84 </conditional>
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85 <output name="output1" file="test_output1.vcf" ftype="vcf" />
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86 </test>
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87 <test>
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88 <param name="input1" value="test_input1.vcf" ftype="vcf" />
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89 <param name="filters" value="close_to_indel_filter" />
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90 <conditional name="filter_options">
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91 <param name="show_filter_options" value="yes" />
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92 <param name="indel_window_size" value="5" />
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93 </conditional>
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94 <output name="output1" file="test_output2.vcf" ftype="vcf" />
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95 </test>
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96 <test>
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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97 <param name="input1" value="test_input1.vcf" ftype="vcf" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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98 <param name="filters" value="min_percentage_alt_filter" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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99 <conditional name="filter_options">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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100 <param name="show_filter_options" value="yes" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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101 <param name="min_percentage_alt" value="95.0" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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102 </conditional>
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103 <output name="output1" file="test_output3.vcf" ftype="vcf" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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104 </test>
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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105 <test>
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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106 <param name="input1" value="test_input2.vcf" ftype="vcf" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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107 <param name="filters" value="min_percentage_alt_filter" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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108 <conditional name="filter_options">
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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109 <param name="show_filter_options" value="yes" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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110 <param name="min_percentage_alt" value="30.0" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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111 </conditional>
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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112 <output name="output1" file="test_output4.vcf" ftype="vcf" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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113 </test>
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114 <test>
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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115 <param name="input1" value="test_input1.vcf" ftype="vcf" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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116 <param name="filters" value="min_depth_filter" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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117 <conditional name="filter_options">
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118 <param name="show_filter_options" value="yes" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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119 <param name="min_depth" value="30" />
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120 </conditional>
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121 <output name="output1" file="test_output5.vcf" ftype="vcf" />
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122 </test>
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123 <test>
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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124 <param name="input1" value="test_input1.vcf" ftype="vcf" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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125 <param name="filters" value="snv_only_filter" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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126 <output name="output1" file="test_output6.vcf" ftype="vcf" />
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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127 </test>
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128 </tests>
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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129 <help><![CDATA[
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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130 This tool offers multiple options for filtering variants (in
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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131 VCF files, relative to M. tuberculosis H37Rv).
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132
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133 It currently has 5 main modes:
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134
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135 1. Filter by region. Mask out variants in certain regions. Region lists available as:
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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136 1. PE/PPE genes from `Fishbein et al 2015 <https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981>`_
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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137 2. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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138 3. `MTBseq <https://github.com/ngs-fzb/MTBseq_source>`_ list of antibiotic resistant genes
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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diff changeset
139 4. `UVP <https://github.com/CPTR-ReSeqTB/UVP>`_ list of repetitive loci in M. tuberculosis genome
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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140 2. Filter by window around indels. Masks out variants within a certain distance (by default 5 bases) of an insertion or deletion site.
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141 3. Filter by percentage of alternate allele bases. Mask out variants with less than a minimum percentage (by default 90%) alternative alleles.
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142 4. Filter by depth of aligned reads.
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143 5. Filter out all variants that are not SNV (single nucleotide variants).
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144
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145 When used together the effects of the filters are added (i.e. a variant is masked out if it is masked by any of the filters).
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146 ]]></help>
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147 <citations>
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148 <citation type="bibtex"><![CDATA[
3b1e7c170b10 "planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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parents:
diff changeset
149 @misc{vanHeusden2019,
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parents:
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150 author = {van Heusden, P.},
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parents:
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151 title = {tb_variant_filter},
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152 year = {2019},
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parents:
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153 publisher = {GitHub},
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parents:
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154 journal = {GitHub repository},
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155 howpublished = {\url{https://github.com/pvanheus/tb_variant_filter}},
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parents:
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156 commit = {4a9b2a4a85ddbfbb0d713a02373c8aa0aa159a6c}
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parents:
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157 }
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parents:
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158 ]]></citation>
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parents:
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159 </citations>
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160 </tool>