view mothur/tools/mothur/bin.seqs.xml @ 32:ec8df51e841a

Fixes courtesy of Peter Briggs: metagenomics.py: - Groups class: Fix for when second column not present - Axes class: make 'sniff' method more sensitive to try and restrict arbitrary tabular data uploads being sniffed as this type mothur_wrapper.py: - update cmd_dict['chimera.perseus'], to use correct inputs - add --beta option (needed for chimera.perseus tool) - add function for converting input floats from scientific notation (e.g. 1e-6, which mothur can't handle) to decimal format (e.g. 0.00001, which it can) chimera.perseus.xml: - add output data item for the "accnos" file (not previous captured in the history) trim.flows.xml: - cosmetic change: base name for additional output data items is now "trim.flows", rather than "logfile" (clarifies history items) shhh.flows.xml: - cosmetic change: update default value specified in help for mindiff to be consistent with that given in the mothur documentation

<tool id="mothur_bin_seqs" name="Bin.seqs" version="1.20.0" 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='$__new_file_path__' 
  --new_datasets='^\S+?\.(unique|[0-9.]*)\.fasta$:${fasta.ext}'
  --fasta=$fasta
  --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
  #if $group.__str__ != "None" and len($group.__str__) > 0:
   --group='$group'
  #end if
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
  <param name="otu" type="data" format="list" label="list - OTU List"/>
  <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options>
    <filter type="data_meta" ref="otu" key="labels" />
   </options>
  </param>
  <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
 </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 bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences.

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

 </help>
</tool>