view mothur/tools/mothur/indicator.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_indicator" name="Indicator" version="1.21.0">
 <description>Identify indicator "species" for nodes on a tree</description>
 <command interpreter="python">
  mothur_wrapper.py 
  ## output {group_file_name}.pick.{label}.groups   {list_file_name}.pick.{label}.list 
  #import re, os.path
  --cmd='indicator'
  --outputdir='$logfile.extra_files_path'
  #if $tree.__str__ != "None" and len($tree.__str__) > 0:
   --tree=$tree
  #end if
  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
   --shared=$otu
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__):
  --relabund=$otu
  #end if
  #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
  #if $design.__str__ != "None" and len($design.__str__) > 0:
   --design=$design
  #end if
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.indicator.tre$:'$tree_out,'^\S+\.indicator.summary$:'$summary
  --processors=8
 </command>
 <inputs>
  <param name="otu" type="data" format="shared,relabund" label="shared/relabund - Otu dataset"/>
  <param name="label" type="select" optional="true" label="label - OTU Labels" >
   <options>
    <filter type="data_meta" ref="otu" key="labels" />
   </options>
  </param>
  <param name="groups" type="select" optional="true" label="groups - Pick groups to annalyze" multiple="true">
   <options>
    <filter type="data_meta" ref="otu" key="groups" />
   </options>
  </param>
  <param name="tree" type="data" format="tree"  optional="true" label="tree - A newick-formatted tree" 
         help="Optional, if a design file is provided."/>
  <param name="design" type="data" format="tabular" optional="true" label="design - assign groups to new grouping"
         help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tre" name="tree_out" label="${tool.name} on ${on_string}: indicator.tre">
   <filter>tree != None</filter>
  </data>
  <data format="tabular" name="summary" label="${tool.name} on ${on_string}: indicator.summary"/>
 </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 indicator_ command reads a shared_ or relabund_ file and a tree file, and outputs a .indicator.summary file and when a tree file is given a .indicator.tre file. The summary file lists the indicator value for each OTU for each node.  The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file. 

.. _shared: http://www.mothur.org/wiki/Shared_file
.. _relabund: http://www.mothur.org/wiki/Get.relabund
.. _indicator: http://www.mothur.org/wiki/Indicator


 </help>
</tool>