<tool id="mothur_create_database" name="Create.database" version="1.27.0" >
 <description>creates a database file from a list, repnames, repfasta and contaxonomy file</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='create.database'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+?\.database$:'$database
  --outputdir='$logfile.extra_files_path'
  ## --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  ## --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy','^\S+?\.(unique|[0-9.]*\.cons\.tax\.summary)$:tax.summary'
  #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
    --shared=$otu
  #else
    --list=$otu
  #end if
  --repfasta=$repfasta
  --repname=$repname
  --contaxonomy=$contaxonomy
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
  #if $group.__str__ != "None" and len($group.__str__) > 0:
   --group='$group'
  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="list,shared" label="list or shared - OTU List of Shared"/>
  <param name="repfasta" type="data" format="fasta" label="repfasta - rep.fasta"
         help="fasta file output by get.oturep"/>
  <param name="repname" type="data" format="names" label="repname - rep.names"
         help="names file output by get.oturep"/>
  <param name="contaxonomy" type="select" format="cons.taxonomy" label="contaxonomy - Consensus Taxonomy"
         help="consensus taxonomy file output by classify.otu"/>
  <param name="group" type="data" format="groups" optional="true" label="group - Groups for summary file"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options>
    <filter type="data_meta" ref="otu" key="labels" />
   </options>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="database" label="${tool.name} on ${on_string}: database" />
 </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 create.database_ command reads a list_ or shared_ file, .cons.taxonomy, .rep.fasta, .rep.names and optional group file, and creates a database file. 

.. _list: http://www.mothur.org/wiki/List_file
.. _shared: http://www.mothur.org/wiki/Shared_file
.. _create.database: http://www.mothur.org/wiki/Create.database


 </help>
</tool>