view mothur/tools/mothur/bin.seqs.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

<tool id="mothur_bin_seqs" name="Bin.seqs" version="1.16.0" force_history_refresh="True">
 <description>Order Sequences by OTU</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='bin.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__' 
  --new_datasets='^\S+?\.(unique|[0-9.]*)\.fasta$:fasta'
  --fasta=$fasta
  --READ_cmd='read.otu'
  --READ_list=$otu
  #if $name.__str__ != "None" and len($name.__str__) > 0:
   --name=$name
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
  <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/>
  <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
   </options>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
 </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 bin.seqs_ command prints out a fasta-formatted file where sequences are ordered according to the OTU that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences.

.. _bin.seqs: http://www.mothur.org/wiki/Bin.seqs

 </help>
</tool>