[2] | 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">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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