<tool id="lca1" name="Find lowest diagnostic rank" version="1.0.1">
  <description></description>
    <requirements>
        <requirement type="package">taxonomy</requirement>
    </requirements>
  <command interpreter="python">
    lca.py $input1 $out_file1 $rank_bound
  </command>
  <inputs>
    <param format="taxonomy" name="input1" type="data" label="for taxonomy dataset"/>
    <param name="rank_bound" label="require the lowest rank to be at least" type="select">
        <option value="0">No restriction</option>
        <option value="3">Superkingdom</option>
        <option value="4">Kingdom</option>
        <option value="5">Subkingdom</option>
        <option value="6">Superphylum</option>
        <option value="7">Phylum</option>
        <option value="8">Subphylum</option>
        <option value="9">Superclass</option>
        <option value="10">Class</option>
        <option value="11">Subclass</option>
        <option value="12">Superorder</option>
        <option value="13">Order</option>
        <option value="14">Suborder</option>
        <option value="15">Superfamily</option>
        <option value="16">Family</option>
        <option value="17">Subfamily</option>
        <option value="18">Tribe</option>
        <option value="19">Subtribe</option>
        <option value="20">Genus</option>
        <option value="21">Subgenus</option>
        <option value="22">Species</option>
        <option value="23">Subspecies</option>
    </param>
  </inputs>
  <outputs>
    <data format="taxonomy" name="out_file1" metadata_source="input1" />
  </outputs>
  <tests>
     <test>
          <param name="input1" value="lca_input.taxonomy" ftype="taxonomy"/>
          <param name="rank_bound" value="0" />
          <output name="out_file1" file="lca_output.taxonomy" ftype="taxonomy"/>
     </test> 
     <test>
          <param name="input1" value="lca_input2.taxonomy" ftype="taxonomy"/>
          <param name="rank_bound" value="7" />
          <output name="out_file1" file="lca_output2.taxonomy" ftype="taxonomy"/>
     </test> 
     
     <!--Test case with invalid lines -->
     <test>
          <param name="input1" value="lca_input3.taxonomy" ftype="taxonomy"/>
          <param name="rank_bound" value="10" />
          <output name="out_file1" file="lca_output3.taxonomy" ftype="taxonomy"/>
     </test> 
 </tests>

 <help>

**What it does**

This tool identifies the lowest taxonomic rank for which a mategenomic sequencing read is diagnostic. It takes datasets produced by *Fetch Taxonomic Ranks* tool (aka Taxonomy format) as the input. 

-------

**Example**

Suppose you have two reads, **read_1** and **read_2**, with the following taxonomic profiles (scroll sideways to see the entire dataset)::
  
    read_1 1 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus1 subgenus1 species1 subspecies1
    read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus2 subgenus2 species2 subspecies2
    read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum3 subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species3 subspecies3
    read_2 4 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum4 subphylum4 superclass4 class4 subclass4 superorder4 order4 suborder4 superfamily4 family4 subfamily4 tribe4 subtribe4 genus4 subgenus4 species4 subspecies4

For **read_1** taxonomic labels are consistent until the genus level, where the taxonomy splits into two branches, one ending with *subspecies1* and the other with *subspecies2*. This implies **that the lowest taxomomic rank read_1 can identify is SUBTRIBE**.  Similarly, read_2 is diagnostic up until the **superphylum** level.  As a results the output of this tool will be::

    read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n
    read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 n       n          n           n      n         n           n      n         n            n       n          n      n         n n n n
    
where, **n** means *EMPTY*. 

--------

**What's up with the drop down?**

Why do we need the *require the lowest rank to be at least* dropdown?  Let's look at the above example again. Suppose you need to find only those reads that are diagnostic on at least phylum level. To do this you need to set the *require the lowest rank to be at least* to **phylum**. As a result your output will look like this::

    read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n

.. class:: infomark
    
Note, that **read_2** is now omitted as it matches two phyla (**phylum3** and **phylum4**) and therefore is not diagnostic (but rather cosmopolitan) on *phylum* level. 





</help>
</tool>