annotate mothur/tools/mothur/shhh.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_shhh_seqs" name="Shhh.seqs" version="1.23.0">
 <description>Denoise program (Quince SeqNoise)</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  --cmd='shhh.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shhh_seqs\.fasta$:'$shhh_fasta,'^\S+\.shhh_seqs\.names$:'$shhh_names,'^\S+\.shhh\.\S+\.map$:'$shhh_map
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  --name=$name
  #if $group.__str__ != "None" and len($group.__str__) > 0:
   --group=$group
  #end if
  #if $sigma.__str__ != '':
   --sigma=$sigma 
  #end if
  --processors=8
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/>
  <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
  <param name="group" type="data" format="groups" optional="true" label="group - Sequences Name reference"/>
  <param name="sigma" type="float" value="" optional="true" label="sigma" 
         help="default .01">
   <validator type="in_range" message="sigma between 0. and 1." min="0.0" max="1.0"/>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="fasta" name="shhh_fasta" label="${tool.name} on ${on_string}: shhh.fasta"/>
  <data format="names" name="shhh_names" label="${tool.name} on ${on_string}: shhh.names"/>
  <data format="txt" name="shhh_map" label="${tool.name} on ${on_string}: shhh.map"/>
 </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 shhh.seqs_ command is a mothur-based rewrite of Chris Quince's sequence denoting program, SeqNoise.  Schloss prefers pre.cluster for this operation.

.. _shhh.seqs: http://www.mothur.org/wiki/Shhh.seqs


 </help>
</tool>