view mothur/tools/mothur/rarefaction.shared.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_rarefaction_shared" name="Rarefaction.shared" version="1.26.0" force_history_refresh="True">
 <description>Generate inter-sample rarefaction curves for OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='rarefaction.shared'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.rarefaction$:'$rarefaction
  --outputdir='$logfile.extra_files_path'
  --shared=$otu
  #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 $design.use:
   --design=$design.design
   #if $design.sets.__str__ != '':
    --sets='$design.sets'  
   #end if
  #end if
  #if int($iters.__str__) > 0:
   --iters=$iters
  #end if
  $jumble
  #if $calc.__str__ != "None" and len($calc.__str__) > 0:
    --calc='$calc'
  #end if
  #if $subsample.use.__str__ == 'yes':
   #if $subsample.subsample.__str__ != '':
     --subsample=$subsample.subsample
   #else
     --subsample=T
   #end if
   #if $subsample.subsampleiters.__str__ != '':
     --subsampleiters=$subsample.subsampleiters
   #end if
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.ave-std\.((unique|[0-9.]*)(\..*?)+\.shared\.rarefaction)$:tabular'
  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options>
    <filter type="data_meta" ref="otu" key="labels" />
   </options>
  </param>
  <param name="groups" type="select" label="groups - Groups to analyze" multiple="true">
   <help>All groups will be analyzed by default if none are selected</help>
   <options>
    <filter type="data_meta" ref="otu" key="groups" />
    <!--
    <filter type="add_value" name="all" value="all" />
    -->
   </options>
  </param>
  <conditional name="design">
    <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label=" run on a per set basis using a design file"/>
    <when value="yes">
    <param name="design" type="data" format="design" label="design - assigns groups to sets" 
           help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
    <param name="sets" type="select" label="sets - group sets to analyze" multiple="true">
     <options>
      <filter type="data_meta" ref="design" key="groups" />
     </options>
    </param>
    </when>
    <when value="no"/>
  </conditional>

  <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/>
  <param name="jumble" type="boolean" truevalue="" falsevalue="--jumble=false" checked="true" label="jumble"/>
  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
   <option value="sharedobserved" selected="true">sharedobserved - the number of sequences in two samples</option>
   <option value="sharednseqs">sharednseqs - the number of sequences in two samples</option>
  </param>
  <conditional name="subsample">
    <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="produce subsample rarefactions"/>
    <when value="yes">
      <param name="subsample" type="integer" value="" optional="true" label="subsample - size pergroup of the sample" 
             help="Leave blank to use the size of your smallest group"/>
      <param name="subsampleiters" type="integer" value="0" optional="true" label="subsampleiters - Number of times to run the subsample"/>
    </when>
    <when value="no"/>
  </conditional>

 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction" />
 </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 rarefaction.shared_ command generates inter-sample rarefaction curves using a re-sampling without replacement approach. The traditional way that ecologists use rarefaction is not to randomize the sampling order within a sample, rather between samples. For instance, if we wanted to know the number of OTUs in the human colon, we might sample from various sites within the colon, and sequence a bunch of 16S rRNA genes. By determining the number of OTUs in each sample and comparing the composition of those samples it is possible to determine how well you have sampled the biodiversity within the individual.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators

.. _rarefaction.shared: http://www.mothur.org/wiki/Rarefaction.shared

 </help>
</tool>