Mercurial > repos > greg > vsnp_get_snps

annotate vsnp_get_snps.xml @ 14:44b84d32883c draft default tip

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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
author greg
date Mon, 15 Nov 2021 23:14:34 +0000
parents cd636b0e4f95
children
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1 <tool id="vsnp_get_snps" name="vSNP: get SNPs" version="@WRAPPER_VERSION@.1+galaxy0" profile="@PROFILE@">
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2 <description></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 <requirements>
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7 <expand macro="openpyxl_requirement"/>
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8 <expand macro="pandas_requirement"/>
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9 <expand macro="pyvcf_requirement"/>
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10 <expand macro="xlrd_requirement"/>
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13 #import re
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14
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15 #set input_vcf_dir = 'input_vcf_dir'
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16 #set output_json_avg_mq_dir = 'output_json_avg_mq_dir'
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17 #set output_json_snps_dir = 'output_json_snps_dir'
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18 #set output_snps_dir = 'output_snps_dir'
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19
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20 mkdir -p $input_vcf_dir &&
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21 mkdir -p $output_json_avg_mq_dir &&
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22 mkdir -p $output_json_snps_dir &&
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23 mkdir -p $output_snps_dir &&
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24
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25 #if str($input_additional_zc_vcf_collection_cond.input_additional_zc_vcf_collection) =='yes':
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26 #set dbkey = '?'
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27 #for $i in $input_additional_zc_vcf_collection_cond.input_vcf_collection:
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28 #if str($dbkey) == '?':
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29 #set dbkey = $i.metadata.dbkey
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30 #else if str($dbkey) != $i.metadata.dbkey:
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cd636b0e4f95 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit cab8ee43e902a3ae7b0fd6b06842c4b5c221af25"
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31 >&2 echo "The dbkeys associated with the zero coverage VCF files with SNPs found in closely related isolate groups are not unique, check ${i.name}" && exit 1
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32 #end if
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33 #set vcf_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
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34 ln -s '${i}' '$input_vcf_dir/${vcf_identifier}' &&
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35 #end for
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36 #if str($dbkey) == '?':
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37 >&2 echo "The dbkey must be set for the zero coverage VCF files with SNPs found in closely related isolate groups" && exit 1
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38 #end if
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39 #end if
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40 #if str($input_zc_vcf_type_cond.input_zc_vcf_type) == "single":
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41 #set zc_vcf_identifier = re.sub('[^\s\w\-]', '_', str($input_zc_vcf.element_identifier))
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42 ln -s '${input_zc_vcf}' '$input_vcf_dir/${zc_vcf_identifier}' &&
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43 #else
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44 #for $i in $input_zc_vcf_type_cond.input_zc_vcf_collection:
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45 #set zc_vcf_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
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46 ln -s '${i}' '$input_vcf_dir/${zc_vcf_identifier}' &&
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47 #end for
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48 #end if
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49 #if str($input_excel_cond.input_excel_param) == 'yes':
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50 #if str($input_excel_cond.excel_source_cond.excel_source) == 'cached':
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51 #set excel_file = 'No genome specified for input VCF (database) file(s)'
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52 #set excel_fields = $__app__.tool_data_tables['vsnp_excel'].get_fields()
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53 ## The value of excel_fields is a nested list that looks like this.
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54 ## [['AF2122', 'Mbovis_define_filter.xlsx', '~/tool-data/vsnp/AF2122/excel/Mbovis_define_filter.xlsx', 'Excel file for AF2122'],...]
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55 #for $i in $excel_fields:
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56 #if str($i[0]) == $dbkey:
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57 #set excel_file = $i[2]
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58 #break
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59 #end if
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60 #end for
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61 #else:
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62 #set excel_file = $input_excel_cond.excel_source_cond.input_excel
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63 #end if
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64 #end if
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65 python '$__tool_directory__/vsnp_get_snps.py'
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66 --ac $ac
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67 #if str($input_excel_cond.input_excel_param) == 'yes':
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68 --input_excel '$excel_file'
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69 #end if
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70 $all_isolates
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71 --input_vcf_dir '$input_vcf_dir'
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72 --min_mq $min_mq
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73 --min_quality_score $min_quality_score
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74 --output_json_avg_mq_dir '$output_json_avg_mq_dir'
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75 --output_json_snps_dir '$output_json_snps_dir'
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76 --output_snps_dir '$output_snps_dir'
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77 --output_summary '$output_summary'
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78 --processes \${GALAXY_SLOTS:-8}
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79 --quality_score_n_threshold $quality_score_n_threshold
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80 --dbkey '$dbkey'
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81 ]]></command>
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82 <inputs>
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83 <conditional name="input_zc_vcf_type_cond">
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84 <param name="input_zc_vcf_type" type="select" label="Choose the category of the files to be analyzed">
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85 <option value="collection" selected="true">A collection of zero coverage VCF files</option>
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86 <option value="single">A single zero coverage VCF file</option>
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87 </param>
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88 <when value="single">
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89 <param name="input_zc_vcf" type="data" format="vcf" label="Zero coverage VCF file"/>
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90 </when>
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91 <when value="collection">
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92 <param name="input_zc_vcf_collection" format="vcf" type="data_collection" collection_type="list" label="Collection of zero coverage VCF files"/>
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93 </when>
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94 </conditional>
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95 <conditional name="input_additional_zc_vcf_collection_cond">
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96 <param name="input_additional_zc_vcf_collection" type="select" label="Include an additional collection of curated zero-coverage VCF files?">
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97 <option value="no" selected="true">No</option>
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98 <option value="yes">Yes</option>
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99 </param>
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100 <when value="no"/>
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101 <when value="yes">
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102 <param name="input_vcf_collection" format="vcf" type="data_collection" collection_type="list" label="Collection of zero coverage VCF files with SNPs found in closely related isolate groups"/>
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103 </when>
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104 </conditional>
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105 <param name="ac" type="integer" min="0" value="2" label="Allele count threshold" help="At least 1 position must have this value for a SNP to be added to a group"/>
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106 <param name="min_mq" type="integer" min="0" value="56" label="Map quality threshold" help="At least 1 position must have a higher MQ value for a SNP to be added to a group"/>
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107 <param name="min_quality_score" type="integer" min="0" value="150" label="Quality score threshold" help="At least 1 position must have a higher quality score for a SNP to be added to a group"/>
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108 <param name="quality_score_n_threshold" type="integer" min="0" value="150" label="Minimum quality score N value for alleles" help="Alleles are marked as N for quality scores between this value and the minimum quality score value above"/>
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109 <conditional name="input_excel_cond">
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110 <param name="input_excel_param" type="select" label="Use Excel file for grouping and filtering?">
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111 <option value="yes" selected="true">Yes</option>
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112 <option value="no">No</option>
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113 </param>
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114 <when value="yes">
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115 <conditional name="excel_source_cond">
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116 <param name="excel_source" type="select" label="Choose the source for the Excel file">
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117 <option value="cached">locally cached</option>
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118 <option value="history">from history</option>
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119 </param>
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120 <when value="cached">
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121 <param name="input_excel" type="select" label="Excel file">
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122 <options from_data_table="vsnp_excel">
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123 <validator type="no_options" message="No built-in Excel grouping and filtering datasets are available"/>
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124 </options>
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125 </param>
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126 </when>
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127 <when value="history">
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128 <param name="input_excel" type="data" format="xlsx" label="Excel file"/>
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129 </when>
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130 </conditional>
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131 </when>
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132 <when value="no"/>
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133 </conditional>
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134 <param name="all_isolates" type="boolean" truevalue="--all_isolates" falsevalue="" checked="true" label="Create a group containing all isolates?"/>
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135 </inputs>
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136 <outputs>
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137 <collection name="snps" type="list" label="${tool.name} on ${on_string} (SNPs)">
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138 <discover_datasets pattern="__name_and_ext__" directory="output_snps_dir"/>
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139 </collection>
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140 <collection name="json_avg_mq" type="list" label="${tool.name} on ${on_string} (average mq)">
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141 <discover_datasets pattern="__name_and_ext__" directory="output_json_avg_mq_dir"/>
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142 </collection>
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143 <collection name="json_snps" type="list" label="${tool.name} on ${on_string} (SNPs as json)">
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144 <discover_datasets pattern="__name_and_ext__" directory="output_json_snps_dir"/>
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145 </collection>
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146 <data name="output_summary" format="html" label="${tool.name} on ${on_string} (summary)"/>
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147 </outputs>
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148 <tests>
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149 <!--
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150 Unfortunately the test files cannot be gzipped since Galaxy changes the file names
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151 to be something like 00-0121_WI_Cervid_99-A_vcf_gz, and the VCF Reader requires
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152 gzipped files to have a .gz extension. The exception is
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153 UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
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154 -->
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155 <!-- A single vcf input, no excel file, all_isolates is False -->
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156 <test expect_num_outputs="4">
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157 <param name="input_zc_vcf_type" value="single"/>
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158 <param name="input_zc_vcf" value="input_zc_vcf.vcf" ftype="vcf" dbkey="89"/>
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159 <param name="input_additional_zc_vcf_collection" value="yes"/>
9
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160 <param name="input_vcf_collection">
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161 <collection type="list">
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162 <element name="SRR8073662_zc.vcf" value="SRR8073662_zc.vcf" dbkey="89"/>
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163 <element name="SRR1792272_zc.vcf" value="SRR1792272_zc.vcf" dbkey="89"/>
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164 </collection>
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165 </param>
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166 <param name="input_excel_param" value="no"/>
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167 <param name="all_isolates" value=""/>
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168 <output_collection name="snps" type="list" count="1">
14
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greg
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169 <element name="all_vcf" ftype="fasta">
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170 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
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diff changeset
171 <has_size value="150"/>
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greg
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172 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
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173 </element>
0
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174 </output_collection>
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175 <output_collection name="json_avg_mq" type="list" count="1">
14
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greg
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diff changeset
176 <element name="all_vcf" ftype="json">
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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177 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
178 <has_size value="551"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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179 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
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180 </element>
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181 </output_collection>
3
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parents: 2
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182 <output_collection name="json_snps" type="list" count="1">
14
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greg
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diff changeset
183 <element name="all_vcf" ftype="json">
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greg
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184 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
185 <has_size value="876"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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186 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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187 </element>
0
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188 </output_collection>
14
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greg
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diff changeset
189 <output name="output_summary" ftype="html">
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greg
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190 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
191 <has_size value="303"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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192 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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193 </output>
0
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194 </test>
9
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greg
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diff changeset
195 <!-- An input collection, no excel file, all_isolates is False -->
3
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greg
parents: 2
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196 <test expect_num_outputs="4">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
197 <param name="input_zc_vcf_type" value="collection"/>
3
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198 <param name="input_zc_vcf_collection">
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199 <collection type="list">
9
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greg
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diff changeset
200 <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
201 <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
202 </collection>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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203 </param>
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544b2ed99a9a Uploaded
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diff changeset
204 <param name="input_additional_zc_vcf_collection" value="yes"/>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
205 <param name="input_vcf_collection">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
206 <collection type="list">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
207 <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
208 <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
209 <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
210 </collection>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
211 </param>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
212 <param name="input_excel_param" value="no"/>
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213 <param name="all_isolates" value=""/>
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diff changeset
214 <output_collection name="snps" type="list" count="1">
14
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diff changeset
215 <element name="all_vcf" ftype="fasta">
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
216 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
217 <has_size value="5226"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
218 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
219 </element>
9
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greg
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diff changeset
220 </output_collection>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
221 <output_collection name="json_avg_mq" type="list" count="1">
14
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diff changeset
222 <element name="all_vcf" ftype="json">
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
223 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
224 <has_size value="24332"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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225 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
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diff changeset
226 </element>
9
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greg
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diff changeset
227 </output_collection>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
228 <output_collection name="json_snps" type="list" count="1">
14
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
229 <element name="all_vcf" ftype="json">
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
230 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
231 <has_size value="38798"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
232 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
233 </element>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
234 </output_collection>
14
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greg
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diff changeset
235 <output name="output_summary" ftype="html">
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
236 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
237 <has_size value="303"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
238 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
239 </output>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
240 </test>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
241 <!-- An input collection, an excel file, all_isolates is False -->
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
242 <test expect_num_outputs="4">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
243 <param name="input_zc_vcf_type" value="collection"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
244 <param name="input_zc_vcf_collection">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
245 <collection type="list">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
246 <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
247 <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
248 </collection>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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249 </param>
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parents: 10
diff changeset
250 <param name="input_additional_zc_vcf_collection" value="yes"/>
9
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greg
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diff changeset
251 <param name="input_vcf_collection">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
252 <collection type="list">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
253 <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
254 <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
255 <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>
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256 </collection>
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257 </param>
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258 <param name="input_excel_param" value="yes"/>
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259 <param name="input_excel" value="89"/>
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260 <param name="all_isolates" value=""/>
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261 <output_collection name="snps" type="list" count="1">
14
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greg
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diff changeset
262 <element name="Mbovis-17" ftype="fasta">
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
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263 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
264 <has_size value="749"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
265 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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266 </element>
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parents: 2
diff changeset
267 </output_collection>
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parents: 2
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268 <output_collection name="json_avg_mq" type="list" count="1">
14
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
269 <element name="Mbovis-17" ftype="json">
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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270 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
271 <has_size value="10884"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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272 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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273 </element>
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274 </output_collection>
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275 <output_collection name="json_snps" type="list" count="1">
14
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
276 <element name="Mbovis-17" ftype="json">
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
277 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
278 <has_size value="6396"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
279 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
280 </element>
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281 </output_collection>
14
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greg
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diff changeset
282 <output name="output_summary" ftype="html">
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
283 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
284 <has_size value="1057"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
285 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
286 </output>
3
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greg
parents: 2
diff changeset
287 </test>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
288 <!-- An input collection, an excel file, all_isolates is True -->
3
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greg
parents: 2
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289 <test expect_num_outputs="4">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
290 <param name="input_zc_vcf_type" value="collection"/>
3
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greg
parents: 2
diff changeset
291 <param name="input_zc_vcf_collection">
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greg
parents: 2
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292 <collection type="list">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
293 <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
294 <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
295 </collection>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
296 </param>
12
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
297 <param name="input_additional_zc_vcf_collection" value="yes"/>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
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diff changeset
298 <param name="input_vcf_collection">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
299 <collection type="list">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
300 <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
301 <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
302 <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>
3
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greg
parents: 2
diff changeset
303 </collection>
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greg
parents: 2
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304 </param>
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parents: 2
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305 <param name="input_excel_param" value="yes"/>
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parents: 2
diff changeset
306 <param name="input_excel" value="89"/>
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greg
parents: 2
diff changeset
307 <param name="all_isolates" value="--all_isolates"/>
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greg
parents: 2
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308 <output_collection name="snps" type="list" count="2">
14
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greg
parents: 13
diff changeset
309 <element name="Mbovis-17" ftype="fasta">
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greg
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diff changeset
310 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
311 <has_size value="749"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
312 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
313 </element>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
314 <element name="all_vcf" ftype="fasta">
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
315 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
316 <has_size value="4920"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
317 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
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diff changeset
318 </element>
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parents: 2
diff changeset
319 </output_collection>
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greg
parents: 2
diff changeset
320 <output_collection name="json_avg_mq" type="list" count="2">
14
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
321 <element name="Mbovis-17" ftype="json">
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
322 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
323 <has_size value="10884"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
324 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
325 </element>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
326 <element name="all_vcf" ftype="json">
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
327 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
328 <has_size value="24332"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
329 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
330 </element>
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greg
parents: 2
diff changeset
331 </output_collection>
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greg
parents: 2
diff changeset
332 <output_collection name="json_snps" type="list" count="2">
14
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
333 <element name="Mbovis-17" ftype="json">
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
334 <assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
335 <has_size value="6396"/>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
336 </assert_contents>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
337 </element>
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
diff changeset
338 <element name="all_vcf" ftype="json">
44b84d32883c "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
greg
parents: 13
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339 <assert_contents>
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340 <has_size value="36466"/>
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341 </assert_contents>
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342 </element>
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343 </output_collection>
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344 <output name="output_summary" ftype="html">
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345 <assert_contents>
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346 <has_size value="1056"/>
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347 </assert_contents>
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348 </output>
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349 </test>
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350 </tests>
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351 <help>
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352 **What it does**
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353
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354 Accepts a zero coverage VCF file produced by the **vSNP: add zero coverage** tool (or a collection of them) along with a collection
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355 of zero coverage VCF files that have been aligned with the same reference and contain SNPs called between closely related isolate groups.
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356 The tool produces fasta files containing SNP alignments, json files containing the SNP positions and additional json files containing
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357 the average map quality values.
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358
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359 The SNP alignments produced by this tool are used to create phylogenetic trees, so larger input collections result in more populated
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360 phylogenetic trees. Both of the json outputs are used by the **vSNP: build tables** tool to produce annotated SNP tables in the form
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361 of Excel spreadsheets.
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362
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363 An Excel spreadsheet containing specified SNPs can optiomally be used to filter desired SNP positions by group. Users can choose a
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364 locally cached Excel spreadsheet or one from their current history.
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365
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366 A SNP is added to a group if it has at least one position with a specified allele count value, a quality score greater than a specified
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367 value, and a map quality greater than a specified value.
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368
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369 If the allele count equals the specified value (2) and the quality score for a SNP position is greater than the minimum quality score
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370 value (150), the alternate allele is called.
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371
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372 However, if the allele count is 1, the position is called ambiguous. Deletions are called when the alternate allele is a gap. If the
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373 quality score is less than or equal to the minimum quality score N value for alleles (150), the allele is marked "N".
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374
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375 **Required Options**
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376
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377 * **Zero coverage VCF file(s)** - Select a single or collection of zero coverage VCF files, typically produced by the **vSNP: add zero coverage** tool, from the current history.
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378 * **Collection of zero coverage VCF files with SNPs found in closely related isolate groups** - Select a dataset collection of zero coverage vcf files from the current history.
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379
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380 **Additional Options**
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381
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382 * **Allele count threshold** - At least 1 position must have an allele count greater than this value for a SNP to be added to a group (2 is optimal).
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383 * **Map quality threshold** - At least 1 position must have a higher MQ value for a SNP to be added to a group (56 is optimal).
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384 * **Quality score threshold** -At least 1 position must have a higher quality score for a SNP to be added to a group (150 is optimal).
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385 * **Minimum quality score N value for alleles** - If none of the avove 3 requirements is met and the quality score is less than or equal to the minimum quality score N value for alleles, the allele is marked "N" (150 is optimal).
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386 * **Use Excel file for grouping and filtering?** - select Yes to filter desired SNP positions by group. A cached Excel spreadsheet provides the most widely used SNP positions for grouping, but a custom spreadhseet can be selected from the current history.
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387 * **Create a group containing all isolates?** - select Yes to output an additional group containing of all isolates.
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388 </help>
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389 <expand macro="citations"/>
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390 </tool>
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391