<tool id="mothur_chimera_check" name="Chimera.check" version="1.20.0" force_history_refresh="True">
 <description>Find putative chimeras using chimeraCheck</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='chimera.check'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.chimeracheck\.chimeras?$:'$out_file
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  --reference=$alignment.template
  #if int($ksize.__str__) > 0:
   --ksize=$ksize
  #end if
  #if int($increment.__str__) > 0:
   --increment=$increment
  #end if
  #if $svg.gen == 'yes':
   --svg=true
   #if $svg.name.__str__ != "None" and len($svg.name.__str__) > 0:
    --name='$svg.name'
   #end if
   #if $svg.as_datasets.__str__ == "yes":
    --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
    --new_datasets='^(\S+)\.chimeracheck\.svg$:svg'
   #end if
  #end if
  --processors=2
 </command>
 <inputs>
  <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/>
  <conditional name="alignment">
   <param name="source" type="select" label="Select Reference Template from" help="">
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>
   <when value="ref">
    <param name="template" type="select" label="reference - Select an alignment database " help="">
     <options from_file="mothur_aligndb.loc">
      <column name="name" index="0" />
      <column name="value" index="1" />
     </options>
    </param>
   </when>
   <when value="hist">
    <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
   </when>
  </conditional>
  <param name="ksize" type="integer" value="7" label="ksize - kmer length to determine differences between sequence fragments (uses default if &lt; 1)"/>
  <param name="increment" type="integer" value="10" label="increment - Increment for window slide on each iteration (uses default if &lt; 1)"
         help="Default is 10, but you may set it up to sequence length minus twice the window."/>
  <conditional name="svg">
   <param name="gen" type="select" label="svg - Generate a SVG plot for each query sequence" help="">
    <option value="no" selected="true">No</option>
    <option value="yes">Yes</option>
   </param>
   <when value="no"/>
   <when value="yes">
    <param name="name" type="data" format="names" optional="true" label="name - Names of queries for which to generate SVG plot"/>
    <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/>
   </when>
  </conditional>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="txt" name="out_file" label="${tool.name} on ${on_string}: chimeracheck.chimeras" />
 </outputs>
 <requirements>
  <requirement type="binary">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

Mothur_, initiated by Dr. Patrick Schloss and his software development team
in the Department of Microbiology and Immunology at The University of Michigan,
provides bioinformatics for the microbial ecology community.

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

The chimera.check_ command identifies putative chimeras using the chimeraCheck approach. It looks at distance of left side of query to it's closest match + distance of right side of query to it's closest match - distance of whole query and its closest match over several windows.  

Note: following the RDP model this method does not determine whether or not a sequence is chimeric, but allows you to determine that based on the IS values produced.

.. _chimera.check: http://www.mothur.org/wiki/Chimera.check


 </help>
</tool>