view mothur/tools/mothur/get.rabund.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_get_rabund" name="Get.rabund" version="1.19.0">
 <description>Get rabund from a otu list or sabund</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='get.rabund'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.rabund$:'$rabund
  --outputdir='$logfile.extra_files_path'
  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__):
   --list=$otu
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__):
   --sabund=$otu
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label=$label
  #end if
  $sorted
 </command>
 <inputs>
  <param name="otu" type="data" format="list,sabund" label="list,sabund - List or Sabund"/>
  <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
   <options>
    <filter type="data_meta" ref="otu" key="labels" />
   </options>
  </param>
  <param name="sorted" type="boolean" checked="false" truevalue="--sorted=true" falsevalue="" label="sorted - sort by abundance" 
    help="By default the data in the rabund file the same order as the OTUs in input, select to sort by abundance."/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
 </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 get.rabund_ command generates an rabund_ file from a list_ or sabund_ file.

.. _rabund: http://www.mothur.org/wiki/Rabund_file
.. _list: http://www.mothur.org/wiki/List_file
.. _sabund: http://www.mothur.org/wiki/Sabund_file
.. _get.rabund: http://www.mothur.org/wiki/Get.rabund


 </help>
</tool>