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1 <tool id="t2t_report" name="Summarize taxonomy" version="1.0.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="1.0.0">taxonomy</requirement>
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5 </requirements>
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6 <command>taxonomy2tree $input 0 /dev/null $out_file1 0</command>
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7 <inputs>
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8 <param format="taxonomy" name="input" type="data" label="Summarize taxonomic representation for"/>
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9 </inputs>
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10 <outputs>
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11 <data format="tabular" name="out_file1" />
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12 </outputs>
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13 <requirements>
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14 <requirement type="binary">taxonomy2tree</requirement>
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15 </requirements>
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16 <tests>
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17 <test>
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18 <param name="input" value="taxonomyGI.taxonomy" ftype="taxonomy"/>
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19 <output name="out_file1" file="t2t_report.tabular"/>
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20 </test>
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21 </tests>
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22
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23
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24 <help>
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25
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26 **What it does**
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27
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28 Given taxonomy representation (produced by *Taxonomy manipulation->Fetch Taxonomic Ranks* tool) this utility computes a summary of all taxonomic ranks.
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29
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30 ------
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31
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32 **Example**
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33
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34 Suppose the *Taxonomy manipulation->Fetch Taxonomic Ranks* generated the following taxonomy representation::
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35
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36 9916 2 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos taurus n
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37 9606 12585 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n
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38
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39 Running this tool will generate the following output::
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40
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41 Rank Rank Name Count
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42 -------------------------------------
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43 root root 2
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44 superkingdom Eukaryota 2
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45 kingdom Metazoa 2
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46 phylum Chordata 2
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47 subphylum Craniata 2
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48 superclass Gnathostomata 2
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49 class Mammalia 2
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50 superorder Euarchontoglires 1
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51 superorder Laurasiatheria 1
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52 order Primates 1
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53 suborder Haplorrhini 1
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54 suborder Ruminantia 1
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55 superfamily Hominoidea 1
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56 family Bovidae 1
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57 family Hominidae 1
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58 subfamily Bovinae 1
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59 genus Bos 1
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60 genus Homo 1
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61 species Bos taurus 1
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62 species Homo sapiens 1
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63
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64 The output is sorted on Rank and then on Rank Name.
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65
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66 .. class:: warningmark
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67
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68 **Note** that this tool omits "**n**" corresponding to ranks missing from NCBI taxonomy. In the above example *Home sapiens* contains the order name (Primates) while *Bos taurus* does not.
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69
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70
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71 </help>
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72 </tool>
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