view mothur/tools/mothur/make.shared_from_biom.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_make_shared_from_biom" name="Make.shared " version="1.25.0" force_history_refresh="True">
 <description>Make a shared file from a biom file</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  --cmd='make.shared'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared$:'$shared
  --outputdir='$logfile.extra_files_path'
  #if $as_datasets.__str__ == "yes":
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund'
  #end if
  --biom=$biom
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
    --groups=$groups
  #end if
 </command>
 <inputs>
  <param name="biom" type="data" format="biom" label="biom -  The Biological Observation Matrix"/>
  <param name="label" type="text" size="40" label="label - to restrict to these OTU Labels" 
     help="multiple labels separated by hyphens, example: unique-0.02-0.04"/>
  <param name="groups" type="text" size="40" label="groups - restrict to these groups"
     help="multiple groups separated by hyphens, example: control-group1-group2"/>
  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each group rabund"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" />
 </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 make.shared_ command takes a list_ and a group_ file and outputs a shared_ file, as well as a rabund_ file for each group.


.. _list: http://www.mothur.org/wiki/List_file
.. _group: http://www.mothur.org/wiki/Group_file
.. _shared: http://www.mothur.org/wiki/Shared_file
.. _rabund: http://www.mothur.org/wiki/Rabund_file
.. _make.shared: http://www.mothur.org/wiki/Make.shared

 </help>
</tool>