annotate vsnp_build_tables.xml @ 9:f641e52353e8 draft

"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
author greg
date Thu, 29 Jul 2021 13:52:48 +0000
parents a5b1e7dcc971
children 14384fd2a7e2
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f641e52353e8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
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1 <tool id="vsnp_build_tables" name="vSNP: build tables" version="@WRAPPER_VERSION@.3+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 <requirement type="package" version="1.79">biopython</requirement>
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8 <requirement type="package" version="0.25.3">pandas</requirement>
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9 <requirement type="package" version="1.4.4">xlsxwriter</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #import re
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f641e52353e8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
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13 #set output_excel_dir = 'output_excel_dir'
f641e52353e8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
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14 #set input_type = $input_type_cond.input_type
f641e52353e8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
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15 mkdir $output_excel_dir &&
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16 #if $input_type == "collection":
f641e52353e8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
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17 #set input_newick_dir = 'input_newick_dir'
f641e52353e8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
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18 mkdir $input_newick_dir &&
f641e52353e8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
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19 #set input_json_avg_mq_dir = 'input_json_avg_mq_dir'
f641e52353e8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
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20 mkdir $input_json_avg_mq_dir &&
f641e52353e8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
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21 #set input_json_dir = 'input_json_dir'
f641e52353e8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
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22 mkdir $input_json_dir &&
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23 #for $i in $input_type_cond.input_avg_mq_json_collection:
f641e52353e8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
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24 #set file_name = $i.file_name
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25 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
f641e52353e8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
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26 ln -s '$file_name' '$input_json_avg_mq_dir/$identifier' &&
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27 #end for
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28 #for $i in $input_type_cond.input_snps_json_collection:
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29 #set file_name = $i.file_name
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30 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
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31 ln -s '$file_name' '$input_json_dir/$identifier' &&
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32 #end for
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33 #for $i in $input_type_cond.input_newick_collection:
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34 #set file_name = $i.file_name
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35 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
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36 ln -s '$file_name' '$input_newick_dir/$identifier' &&
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37 #end for
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38 #end if
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39 python '$__tool_directory__/vsnp_build_tables.py'
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40 #if $input_type == "single":
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41 --input_avg_mq_json '$input_avg_mq_json'
f641e52353e8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
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42 --input_snps_json '$input_snps_json'
f641e52353e8 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables commit 1131a7accc36df73eac621f6ae8aa3cb62403bde"
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43 --input_newick '$input_newick'
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44 #end if:
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45 #if str($gbk_cond.gbk_param) == "yes":
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46 #set gbk_source_cond = $gbk_cond.gbk_source_cond
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47 #set gbk_source = $gbk_source_cond.gbk_source
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48 #if str($gbk_source) == "cached":
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49 --gbk_file '$gbk_source_cond.gbk_file.fields.path'
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50 #else:
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51 --gbk_file '$gbk_source_cond.gbk_file'
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52 #end if
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53 #end if
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54 --processes \${GALAXY_SLOTS:-8}
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55 ]]></command>
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56 <inputs>
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57 <conditional name="input_type_cond">
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58 <param name="input_type" type="select" label="Choose the category for the files to be analyzed">
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59 <option value="single" selected="true">Single files</option>
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60 <option value="collection">Collection of files</option>
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61 </param>
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62 <when value="single">
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63 <param name="input_snps_json" type="data" format="json" label="SNPs json file"/>
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64 <param name="input_avg_mq_json" type="data" format="json" label="Average MQ json file"/>
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65 <param name="input_newick" type="data" format="newick" label="Best-scoring ML tree file"/>
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66 </when>
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67 <when value="collection">
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68 <param name="input_snps_json_collection" format="json" type="data_collection" collection_type="list" label="Collection of SNPs json files"/>
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69 <param name="input_avg_mq_json_collection" format="json" type="data_collection" collection_type="list" label="Collection of average MQ json files"/>
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70 <param name="input_newick_collection" format="newick" type="data_collection" collection_type="list" label="Collection of best-scoring ML tree files"/>
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71 </when>
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72 </conditional>
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73 <conditional name="gbk_cond">
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74 <param name="gbk_param" type="select" label="Use Genbank file?">
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75 <option value="yes" selected="true">yes</option>
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76 <option value="no">No</option>
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77 </param>
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78 <when value="yes">
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79 <conditional name="gbk_source_cond">
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80 <param name="gbk_source" type="select" label="Choose the source for the Genbank file">
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81 <option value="cached" selected="true">locally cached</option>
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82 <option value="history">from history</option>
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83 </param>
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84 <when value="cached">
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85 <param name="gbk_file" type="select" label="Genbank file">
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86 <options from_data_table="vsnp_genbank">
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87 <validator type="no_options" message="A cached Genbank file is not available for the build associated with the selected average MQ json file"/>
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88 </options>
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89 </param>
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90 </when>
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91 <when value="history">
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92 <param name="gbk_file" type="data" format="genbank" label="Genbank file">
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93 <validator type="no_options" message="The current history does not include a genbank dataset"/>
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94 </param>
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95 </when>
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96 </conditional>
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97 </when>
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98 <when value="no"/>
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99 </conditional>
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100 </inputs>
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101 <outputs>
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102 <collection name="excel" type="list" format="xlsx" label="${tool.name} on ${on_string}">
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103 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;xlsx)" directory="output_excel_dir"/>
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104 </collection>
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105 </outputs>
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106 <tests>
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107 <test>
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108 <param name="input_snps_json" value="input_snps_json.json" ftype="json" dbkey="89"/>
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109 <param name="input_newick" value="input_newick.newick" ftype="newick" dbkey="89"/>
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110 <param name="input_avg_mq_json" value="input_avg_mq_json.json" ftype="json" dbkey="89"/>
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111 <param name="gbk_param" value="no"/>
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112 <output_collection name="excel" type="list" count="2">
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113 <element name="cascade_table" file="cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
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114 <element name="sort_table" file="sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
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115 </output_collection>
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116 </test>
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117 <test>
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118 <param name="input_type" value="collection"/>
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119 <param name="input_snps_json_collection">
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120 <collection type="list">
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121 <element name="Mbovis-01_snps.json" value="Mbovis-01_snps.json" dbkey="89"/>
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122 <element name="Mbovis-01D_snps.json" value="Mbovis-01D_snps.json" dbkey="89"/>
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123 <element name="Mbovis-01D6_snps.json" value="Mbovis-01D6_snps.json" dbkey="89"/>
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124 </collection>
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125 </param>
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126 <param name="input_newick_collection">
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127 <collection type="list">
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128 <element name="Mbovis-01_snps.newick" value="Mbovis-01_snps.newick" dbkey="89"/>
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129 <element name="Mbovis-01D_snps.newick" value="Mbovis-01D_snps.newick" dbkey="89"/>
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130 <element name="Mbovis-01D6_snps.newick" value="Mbovis-01D6_snps.newick" dbkey="89"/>
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131 </collection>
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132 </param>
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133 <param name="input_avg_mq_json_collection">
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134 <collection type="list">
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135 <element name="Mbovis-01_snps.json" value="Mbovis-01_avg_mq.json" dbkey="89"/>
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136 <element name="Mbovis-01D_snps.json" value="Mbovis-01D_avg_mq.json" dbkey="89"/>
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137 <element name="Mbovis-01D6_snps.json" value="Mbovis-01D6_avg_mq.json" dbkey="89"/>
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138 </collection>
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139 </param>
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140 <param name="gbk_param" value="no"/>
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141 <output_collection name="excel" type="list" count="6">
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142 <element name="Mbovis-01D6_snps_newick_cascade_table" file="Mbovis-01D6_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
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143 <element name="Mbovis-01D6_snps_newick_sort_table" file="Mbovis-01D6_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
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144 <element name="Mbovis-01D_snps_newick_cascade_table" file="Mbovis-01D_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
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145 <element name="Mbovis-01D_snps_newick_sort_table" file="Mbovis-01D_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
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146 <element name="Mbovis-01_snps_newick_cascade_table" file="Mbovis-01_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
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147 <element name="Mbovis-01_snps_newick_sort_table" file="Mbovis-01_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
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148 </output_collection>
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149 </test>
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150 </tests>
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151 <help>
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152 **What it does**
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153
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154 Accepts a combination of single SNPs json, average MQ json and newick files (or associated collections of
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155 each) to produce annotated SNPs tables in the form of Excel spreadsheets. The SNPs json and average MQ json
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156 files are typically produced by the **vSNP: get SNPs** tool and the newick files are typically produced by
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157 the **Phyogenetic reconstruction with RaXML** tool.
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158
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159 The SNPs tables display closely related isolates and enables identification of mixed SNPs when multiple
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160 bacterial strains are infecting an organism. The table structure is shown below. The columns identify the
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161 genome location of the SNP calls and the isolates are contained within the rows. The reference (or ancestral
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162 strain if the reference is an outgroup) is listed across the top, identified as the "reference call". SNPs
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163 that are not highlighted will match the reference. The map-quality row values are the average of the map
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164 quality scores of each isolate in that position. These scores measure the confidence that the read has been
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165 mapped to the correct location on the genome. The maximum score possible is 60, and lower scores lessen the
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166 confidence that the SNP was correctly identified. The annotation of the position is provided at the bottom
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167 of the table.
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168
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169 .. image:: table_description.png
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170
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171 SNPs are sorted according to their evolutionary age within the table. The oldest SNPs (encompassing the most
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172 isolates) are furthest to the left. This sorting is somewhat crude - the intent is to improve readibility or
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173 more easily match a related tree.
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174
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175 For a more detailed discussion, see the **Validating and correcting SNP calls** section of
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176 the `vSNP documentation`_.
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177
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178 .. _vSNP documentation: https://github.com/USDA-VS/vSNP/blob/master/docs/detailed_usage.md
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179
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180 **Required Options**
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181
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182 * **Choose the category for the files to be analyzed** - select "Single files" or "Collections of files", then select the appropriate history items (single SNPs json, average MQ json and newick files, or collections of each) based on the selected option.
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183 * **Use Genbank file** - Select "yes" to annotate the tables using the information in the Genbank file. Locally cached files, if available, provide the most widely used annotations, but more custom Genbank files can be chosen from the current history.
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184 </help>
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185 <expand macro="citations"/>
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186 </tool>
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187