view mothur/tools/mothur/deunique.seqs.xml @ 36:040410b8167e default tip

Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.

<tool id="mothur_deunique_seqs" name="Deunique.seqs" version="1.21.0">
 <description>Return all sequences</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='deunique.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.redundant\.fasta$:'$out_fasta,'^\S+\.groups$:'$groups_file
  --outputdir='$logfile.extra_files_path'
	--fasta=$fasta
	#if isinstance($names.datatype, $__app__.datatypes_registry.get_datatype_by_extension('count_table').__class__):
		--count=$names
	#else
		--name=$names
	#end if
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
	<param name="names" type="data" format="names,count_table" label="provide a names file OR a count file" help="A names file will generate a new faste file containing all the sequences. If a group file contains group information, a group file will also be created."/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta"/>
	<data format="groups" name="groups_file" label="${tool.name} on ${on_string}: groups">
		<filter>(isinstance($names.datatype, $__app__.datatypes_registry.get_datatype_by_extension('count_table').__class__))</filter>
	</data>
 </outputs>
 <requirements>
  <requirement type="package" version="1.33">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 deunique.seqs_ command is the reverse of the unique.seqs command, and creates a fasta file from a fasta and name_ file.

.. _name: http://www.mothur.org/wiki/Name_file
.. _deunique.seqs: http://www.mothur.org/wiki/Deunique.seqs

v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output


 </help>
</tool>