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changeset 0:592acb9505fc draft default tip

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Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:26:17 -0500
parents
children
files t2t_report.xml test-data/t2t_report.tabular test-data/taxonomyGI.taxonomy tool_dependencies.xml
diffstat 4 files changed, 98 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/t2t_report.xml	Mon Jan 27 09:26:17 2014 -0500
@@ -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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/t2t_report.tabular	Mon Jan 27 09:26:17 2014 -0500
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomyGI.taxonomy	Mon Jan 27 09:26:17 2014 -0500
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jan 27 09:26:17 2014 -0500
@@ -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>