view mothur/tools/mothur/chimera.ccode.xml @ 12:2088a8d469c9 draft

Fix datatype defs - metagenomics.py

<tool id="mothur_chimera_ccode" name="Chimera.ccode" version="1.20.0">
 <description>Find putative chimeras using ccode</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='chimera.ccode'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.ccode\.chimeras?$:'$out_file,'^\S+\.ccode\.accnos$:'$out_accnos
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  --reference=$alignment.template
  $filter
  #if $mask.source == 'default':
   --mask=default
  #elif $mask.source == 'history':
   --mask=$mask.input
  #end if
  #if int($window.__str__) > 0:
   --window=$window
  #end if
  #if int($numwanted.__str__) > 0:
   --numwanted=$numwanted
  #end if
  --processors=8
 </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="filter" type="boolean" falsevalue="" truevalue="--filter=true" checked="false" label="filter - Apply a 50% soft vertical filter"/>
  <!-- mask -->
  <conditional name="mask">
   <param name="source" type="select" label="Mask option">
    <option value="">None</option>
    <option value="default">default ecoli mask</option>
    <option value="history">From Your History</option>
   </param>
   <when value=""/>
   <when value="default"/>
   <when value="history">
    <param name="input" type="data" format="filter" label="Mask for the reference file" help=""/>
   </when>
  </conditional>
  <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed (default if &lt; 1)" 
         help="Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length."/>
  <param name="numwanted" type="integer" value="20" label="numwanted - Number of sequences compared with each query (uses default if set to 0)"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="txt" name="out_file" label="${tool.name} on ${on_string}: ccode.chimeras" />
  <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: ccode.accnos" />
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">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.ccode_ command identifies putative chimeras using the ccode approach (Chimera and Cross-Over Detection and Evaluation).  Ccode_ compares differences in distances, for each word, between query sequence and reference sequences, and reference sequences and themselves.

This method was written using the algorithms described in the paper_ "Evaluating putative chimeric sequences from PCR-amplified products" by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.

The program can analyze sequences for any required word length. Generally, values of 5-20% of sequence length appear to deliver accurate results, for example, working on 16S rDNA sequences with a full-length of #1500 nt. It should be noted that the use of fragments either too long or too short might result in a reduction of sensitivity.

.. _Ccode: http://www.microextreme.net/downloads.html
.. _paper: http://bioinformatics.oxfordjournals.org/content/21/3/333.full.pdf
.. _chimera.ccode: http://www.mothur.org/wiki/Chimera.ccode


 </help>
</tool>