Mercurial > repos > earlhaminst > ete

annotate ete_lineage_generator.xml @ 16:e4d5d9a69c9d draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit a0d7ab86b86bb764e457767bf8e8bc29868d0cbb
author earlhaminst
date Mon, 10 Mar 2025 23:28:17 +0000
parents 1e85af7a29c4
children
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16
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earlhaminst
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1 <tool id="ete_lineage_generator" name="ETE lineage generator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2
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2 <description>from a list of species/taxids using the ETE Toolkit</description>
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3 <macros>
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4 <import>ete_macros.xml</import>
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5 </macros>
14
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6 <expand macro="bio_tools"/>
2
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 python '$__tool_directory__/ete_lineage_generator.py'
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10 -s '$speciesFile'
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11 -d '$database'
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12 -o '$outputFile'
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13 #if $ranks.levels == "full"
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14 -f
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15 #elif $ranks.levels == "manual"
4
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16 #for $rank in str($ranks.manualranks).split(','):
2
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17 -r $rank
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18 #end for
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19 #end if
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20 #if $compresscond.compress == "-c"
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21 $compresscond.compress
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22 $compresscond.lower
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23 #end if
6
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24 $includeid
2
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25 ]]></command>
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26 <inputs>
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27 <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species/taxid per line" />
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28 <param name="database" type="data" format="sqlite" label="(ETE3) Taxonomy Database" help="The sqlite formatted Taxonomy used by ETE3 (which is derived from NCBI taxonomy)" />
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29 <conditional name="ranks">
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30 <param name="levels" type="select" label="Taxonomic levels" help="Taxonomic levels to include in the output">
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31 <option value="primary" selected="true">Primary</option>
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32 <option value="full">Full</option>
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33 <option value="manual">Manual</option>
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34 </param>
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35 <when value="manual">
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36 <param name="manualranks" type="select" multiple="true" optional="false" label="Manual selection of ranks">
2
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37 <option value="superkingdom">superkingdom</option>
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38 <option value="kingdom" selected="true">kingdom</option>
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39 <option value="subkingdom">subkingdom</option>
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40 <option value="superphylum">superphylum</option>
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41 <option value="phylum" selected="true">phylum</option>
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42 <option value="subphylum">subphylum</option>
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43 <option value="superclass">superclass</option>
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44 <option value="class" selected="true">class</option>
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45 <option value="subclass">subclass</option>
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46 <option value="infraclass">infraclass</option>
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47 <option value="cohort">cohort</option>
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48 <option value="superorder">superorder</option>
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49 <option value="order" selected="true">order</option>
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50 <option value="suborder">suborder</option>
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51 <option value="infraorder">infraorder</option>
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52 <option value="parvorder">parvorder</option>
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53 <option value="superfamily">superfamily</option>
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54 <option value="family" selected="true">family</option>
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55 <option value="subfamily">subfamily</option>
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56 <option value="tribe">tribe</option>
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57 <option value="subtribe">subtribe</option>
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58 <option value="genus" selected="true">genus</option>
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59 <option value="subgenus">subgenus</option>
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60 <option value="species group">species group</option>
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61 <option value="species subgroup">species subgroup</option>
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62 <option value="species" selected="true">species</option>
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63 <option value="subspecies">subspecies</option>
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64 <option value="varietas">varietas</option>
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65 <option value="forma">forma</option>
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66 </param>
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67 </when>
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68 <when value="primary" />
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69 <when value="full" />
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70 </conditional>
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71 <conditional name="compresscond">
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72 <param name="compress" type="select" label="Fill unnamed ranks" help="Fill unnamed ranks with super/sub ranks (see -l)">
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73 <option value="-c" selected="True">Yes</option>
2
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74 <option value="">No</option>
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75 </param>
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76 <when value="-c">
6
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77 <param name="lower" type="boolean" truevalue="-l" falsevalue="" checked="False" label="Prefer lower ranks" help="Take the next available lower rank (default: higher)"/>
2
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78 </when>
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79 <when value="" />
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80 </conditional>
6
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81 <param name="includeid" type="boolean" truevalue="--includeid" falsevalue="" label="Include taxid in the table"
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82 help="For the case when the input consists of taxon names" />
2
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83 </inputs>
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84 <outputs>
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85 <data name="outputFile" format="tsv" label="${tool.name} on ${on_string}"/>
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86 </outputs>
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87 <tests>
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88 <test>
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89 <param name="speciesFile" ftype="txt" value="species.txt" />
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90 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
16
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91 <conditional name="compresscond">
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92 <param name="compress" value="" />
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93 </conditional>
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94 <conditional name="ranks">
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95 <param name="levels" value="full" />
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96 </conditional>
2
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97 <output name="outputFile" file="lineage.txt" />
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98 </test>
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99 <test>
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100 <param name="speciesFile" ftype="txt" value="species.txt" />
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101 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
16
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102 <conditional name="compresscond">
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103 <param name="compress" value="-c" />
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104 </conditional>
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105 <conditional name="ranks">
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106 <param name="levels" value="primary" />
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107 </conditional>
2
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108 <output name="outputFile" file="lineage-compress.txt" />
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109 </test>
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110 <test>
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111 <param name="speciesFile" ftype="txt" value="species.txt" />
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112 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
16
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113 <conditional name="compresscond">
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114 <param name="compress" value="-c" />
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115 <param name="lower" value="true" />
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116 </conditional>
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117 <conditional name="ranks">
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118 <param name="levels" value="primary" />
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119 </conditional>
2
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120 <output name="outputFile" file="lineage-compress-lower.txt" />
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121 </test>
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122 <test>
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123 <param name="speciesFile" ftype="txt" value="species.txt" />
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124 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
16
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125 <conditional name="compresscond">
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126 <param name="compress" value="" />
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127 </conditional>
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128 <conditional name="ranks">
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129 <param name="levels" value="manual" />
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130 <param name="manualranks" value="kingdom,family" />
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131 </conditional>
2
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132 <output name="outputFile" file="lineage-full.txt" />
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133 </test>
6
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134 <test>
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135 <param name="speciesFile" ftype="txt" value="species.txt" />
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136 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
16
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137 <param name="includeid" value="true" />
6
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138 <output name="outputFile" file="lineage-wid.txt" />
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139 </test>
11
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140 <test>
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141 <param name="speciesFile" ftype="txt" value="species_ids.txt" />
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142 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
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143 <output name="outputFile">
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144 <assert_contents>
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145 <has_line line="9606&#009;Eukaryota&#009;Chordata&#009;Mammalia&#009;Euarchontoglires&#009;Hominoidea&#009;Homo&#009;Homo sapiens"/>
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146 <has_line line="0&#009;NA&#009;NA&#009;NA&#009;NA&#009;NA&#009;NA&#009;NA"/>
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147 </assert_contents>
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148 </output>
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149 <assert_stderr>
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150 <has_line line="[0] could not determine lineage!"/>
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151 </assert_stderr>
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152 </test>
2
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153 </tests>
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154 <help><![CDATA[
3
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155 Generates a table with lineage information for a list of species (also taxids and arbitrary taxons are accepted) using the `ETE Toolkit`_.
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156
15
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157 .. _ETE Toolkit: https://etetoolkit.org/
2
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158
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159 **Input**
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160
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161 - *Species file* a single column tabular file
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162 - *(ETE3) Taxonomy Database* a sqlite database that has been created by ETE from the NCBI taxonomy dump
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163
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164 **Options**
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165
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166 - *Taxonomic levels* the columns to be incuded in the output table. There are two presets (full and primary)
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167
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168 - *Full* contains all 29 ranks included in the NCBI taxonomy
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169 - *Primary* contains the primary ranks (kingdom, phylum, class, order, family, genus, species)
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170 - *Manual* the ranks of interest can be chosen by the user. The primary levels are chosen by default.
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171
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172 - *Fill unnamed ranks* Get missing data from "nearby" levels:
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173
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174 - Some nodes in the NCBI taxonomy tree have no name (no rank) these are shown by default as "NA" in the output. If the *compress* option is selected then the rank is accepted if the level name is included (e.g. superorder is accepted as order if the order is unnamed but the name of the superorder is given)
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175
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176 - *Prefer lower ranks for filling* for compressing lower levels are prefered over higher ones
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177
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178 **Output**
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179
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180 Table (tab separated). The first column contains the species names. The following columns contain the
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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181 rank names of the levels of interest.
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182 ]]></help>
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183 <expand macro="citations" />
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184 </tool>