view mothur/tools/mothur/get.otulabels.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_otulabels" name="Get.otulabels" version="1.26.0">
 <description>Selects OTU labels</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
  ## adds .pick before the last extension to the input file
  --cmd='get.otulabels'
  --outputdir='$logfile.extra_files_path'
  --accnos=$accnos
  #if $constaxonomy_in.__str__ != "None" and len($constaxonomy_in.__str__) > 0:
   --constaxonomy=$constaxonomy_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($constaxonomy_in.__str__)) + ":'" + $constaxonomy_out.__str__]
  #end if
  #if $otucorr_in.__str__ != "None" and len($otucorr_in.__str__) > 0:
   --otucorr=$otucorr_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($otucorr_in.__str__)) + ":'" + $otucorr_out.__str__]
  #end if
  #if $corraxes_in.__str__ != "None" and len($corraxes_in.__str__) > 0:
   --corraxes=$corraxes_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($corraxes_in.__str__)) + ":'" + $corraxes_out.__str__]
  #end if
  --result=#echo ','.join($results)
 </command>
 <inputs>
  <param name="accnos" type="data" format="otulabels" label="accnos - otulabels" help="At least one of constaxonomy, otucorr, or corraxes must be given"/>
  <param name="constaxonomy_in" type="data" format="cons.taxonomy" optional="true" label="constaxonomy - Consensus Taxonomy from classify.otu"/>
  <param name="otucorr_in" type="data" format="otu.corr" optional="true" label="otucorr -  OTU correlation from otu.association"/>
  <param name="corraxes_in" type="data" format="axes" optional="true" label="corraxes - axes from corr.axes"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <!-- format should be set to match input -->
  <data format_source="constaxonomy_in" name="constaxonomy_out" label="${tool.name} on ${on_string}: pick.cons.taxonomy">
   <filter>constaxonomy_in != None</filter>
  </data>
  <!-- format should be set to match input -->
  <data format_source="otucorr_in" name="otucorr_out" label="${tool.name} on ${on_string}: pick.otu.corr">
   <filter>otucorr_in != None</filter>
  </data>
  <data format_source="constaxonomy_in" name="constaxonomy_out" label="${tool.name} on ${on_string}: pick.cons.taxonomy">
   <filter>constaxonomy_in != None</filter>
  </data>
 </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.otulabels_ command selects otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected.

.. _classify.otu: http://www.mothur.org/wiki/Classify.otu
.. _corr.axes: http://www.mothur.org/wiki/Corr.axes
.. _otu.association: http://www.mothur.org/wiki/Otu.association
.. _get.otulabels: http://www.mothur.org/wiki/Get.otulabels

 </help>
</tool>