<tool id="find_diag_hits" name="Find diagnostic hits" version="1.0.0">
    <description></description>
    <requirements>
        <requirement type="package">taxonomy</requirement>
    </requirements>
    <command interpreter="python">find_diag_hits.py $input1 $id_col $rank_list $out_format $out_file1</command>
    <inputs>
        <param format="taxonomy" name="input1" type="data" label="Find diagnostic hits in"/>
        <param name="id_col" type="data_column" data_ref="input1" numerical="False" label="Select column with sequence id" />
        <param name="rank_list" type="select" display="checkboxes" multiple="true" label="select taxonomic ranks">
            <option value="superkingdom">Superkingdom</option>
            <option value="kingdom">Kingdom</option>
            <option value="subkingdom">Subkingdom</option>
            <option value="superphylum">Superphylum</option>
            <option value="phylum">Phylum</option>
            <option value="subphylum">Subphylum</option>
            <option value="superclass">Superclass</option>
            <option value="class">Class</option>
            <option value="subclass">Subclass</option>
            <option value="superorder">Superorder</option>
            <option value="order">Order</option>
            <option value="suborder">Suborder</option>
            <option value="superfamily">Superfamily</option>
            <option value="family">Family</option>
            <option value="subfamily">Subfamily</option>
            <option value="tribe">Tribe</option>
            <option value="subtribe">Subtribe</option>
            <option value="genus">Genus</option>
            <option value="subgenus">Subgenus</option>
            <option selected="true" value="species">Species</option>
            <option value="subspecies">Subspecies</option>
        </param>
        <param name="out_format" type="select" label="Select output format">
            <option value="reads">Diagnostic read list</option>
            <option value="counts">Number of diagnostic reads per taxonomic rank</option>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="out_file1" />
    </outputs>
      <tests>
    <test>
      <param name="input1" value="taxonomyGI.taxonomy" ftype="taxonomy"/>
      <param name="id_col" value="1" />
      <param name="rank_list" value="order,genus" />
      <param name="out_format" value="counts" />
      <output name="out_file1" file="find_diag_hits.tabular" />
    </test> 
  </tests>

    
<help>

**What it does**

When performing metagenomic analyses it is often necessary to identify sequence reads corresponding to a particular taxonomic group, or, in other words, diagnostic of a particular taxonomic rank. This utility performs this analysis. It takes data generated by *Taxonomy manipulation->Fetch Taxonomic Ranks* as input and outputs either a list of sequence reads unique to a particular taxonomic rank, or a list of taxonomic ranks and the count of unique reads corresponding to each rank. 

------

**Example**

Suppose the *Taxonomy manipulation->Fetch Taxonomic Ranks* generated the following taxonomy representation::

    read1 2      root Eukaryota Metazoa n n Chordata   Craniata Gnathostomata Mammalia n        Laurasiatheria   n           Ruminantia  n             Bovidae     Bovinae      n          n          Bos        n Bos taurus        n
    read2 12585	 root Eukaryota Metazoa n n Chordata   Craniata Gnathostomata Mammalia n        Euarchontoglires Primates	 Haplorrhini Hominoidea    Hominidae   n            n          n          Homo       n Homo sapiens      n 
    read1 58615  root Eukaryota Metazoa n n Arthropoda n        Hexapoda      Insecta  Neoptera Amphiesmenoptera Lepidoptera Glossata    Papilionoidea Nymphalidae Nymphalinae  Melitaeini Phyciodina Anthanassa n Anthanassa otanes n 
    read3 56785	 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 with the following parameters:

  * *Select column with sequence id* set to **c1**
  * *Select taxonomic ranks* with **order**, and **genus** checked
  * *Output format* set to **Diagnostic read list**
  
will return::

    read2 Primates order
    read3 Primates order
    read2 Homo     genus
    read3 Homo     genus
    
Changing *Output format* set to **Number of diagnostic reads per taxonomic rank** will produce::

    Primates 2       order
    Homo     2       genus
    
.. class:: infomark

Note that **read1** is omitted because it is non-unique: it hits Mammals and Insects at the same time.    

--------

.. class:: warningmark

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>