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Imported from capsule None |
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t2t_report.xml test-data/t2t_report.tabular test-data/taxonomyGI.taxonomy tool_dependencies.xml |
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| diff -r 000000000000 -r 592acb9505fc t2t_report.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/t2t_report.xml Mon Jan 27 09:26:17 2014 -0500 |
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| @@ -0,0 +1,72 @@ +<tool id="t2t_report" name="Summarize taxonomy" version="1.0.0"> + <description></description> + <requirements> + <requirement type="package" version="1.0.0">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> |
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| diff -r 000000000000 -r 592acb9505fc test-data/t2t_report.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t2t_report.tabular Mon Jan 27 09:26:17 2014 -0500 |
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| @@ -0,0 +1,15 @@ +root root 5 +superkingdom Eukaryota 5 +kingdom Metazoa 5 +phylum Chordata 5 +subphylum Craniata 5 +superclass Gnathostomata 5 +class Mammalia 5 +superorder Euarchontoglires 4 +order Primates 4 +suborder Haplorrhini 3 +superfamily Hominoidea 3 +family Hominidae 3 +genus Homo 2 +species Homo sapiens 2 +subspecies Homo sapiens neanderthalensis 1 |
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| diff -r 000000000000 -r 592acb9505fc test-data/taxonomyGI.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomyGI.taxonomy Mon Jan 27 09:26:17 2014 -0500 |
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| @@ -0,0 +1,5 @@ +9606 9606 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n 12583 +40674 40674 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n n n n n n n n n n n n n 410771 +63221 63221 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens Homo sapiens neanderthalensis 2286205 +9604 9604 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n n n n n 23236241 +9443 9443 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates n n n n n n n n n n 33001686 \ No newline at end of file |
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| diff -r 000000000000 -r 592acb9505fc tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jan 27 09:26:17 2014 -0500 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="taxonomy" version="1.0.0"> + <repository changeset_revision="c011d4659306" name="package_taxonomy_1_0_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |