/tools/taxonomy/t2t_report.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 72 lines · 57 code · 15 blank · 0 comment · 0 complexity · f71314c963079098ff6190e4d64e6fe6 MD5 · raw file
- <tool id="t2t_report" name="Summarize taxonomy" version="1.0.0">
- <description></description>
- <requirements>
- <requirement type="package">taxonomy</requirement>
- </requirements>
- <command>taxonomy2tree $input 0 /dev/null $out_file1 0</command>
- <inputs>
- <param format="taxonomy" name="input" type="data" label="Summarize taxonomic representation for"/>
- </inputs>
- <outputs>
- <data format="tabular" name="out_file1" />
- </outputs>
- <requirements>
- <requirement type="binary">taxonomy2tree</requirement>
- </requirements>
- <tests>
- <test>
- <param name="input" value="taxonomyGI.taxonomy" ftype="taxonomy"/>
- <output name="out_file1" file="t2t_report.tabular"/>
- </test>
- </tests>
-
- <help>
- **What it does**
- Given taxonomy representation (produced by *Taxonomy manipulation->Fetch Taxonomic Ranks* tool) this utility computes a summary of all taxonomic ranks.
- ------
- **Example**
- Suppose the *Taxonomy manipulation->Fetch Taxonomic Ranks* generated the following taxonomy representation::
- 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
- 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
- Running this tool will generate the following output::
-
- Rank Rank Name Count
- -------------------------------------
- root root 2
- superkingdom Eukaryota 2
- kingdom Metazoa 2
- phylum Chordata 2
- subphylum Craniata 2
- superclass Gnathostomata 2
- class Mammalia 2
- superorder Euarchontoglires 1
- superorder Laurasiatheria 1
- order Primates 1
- suborder Haplorrhini 1
- suborder Ruminantia 1
- superfamily Hominoidea 1
- family Bovidae 1
- family Hominidae 1
- subfamily Bovinae 1
- genus Bos 1
- genus Homo 1
- species Bos taurus 1
- species Homo sapiens 1
-
- The output is sorted on Rank and then on Rank Name.
- .. class:: warningmark
- **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.
- </help>
- </tool>