annotate mothur/tools/mothur/rarefaction.single.xml @ 33:d53b9eb16c2d

mothur_wrapper.py - convert_value needs to return a String

<tool id="mothur_rarefaction_single" name="Rarefaction.single" version="1.20.0" force_history_refresh="True">
 <description>Generate intra-sample rarefaction curves for OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='rarefaction.single'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  #if $as_datasets.__str__ == 'yes':
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.(((\S+)\.)?(rarefaction|r_\w*))$:tabular'
  #end if
  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
   --shared=$otu
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
   --rabund=$otu
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__):
   --sabund=$otu
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__):
   --list=$otu
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
  #if $calc.__str__ != "None" and len($calc.__str__) > 0:
    --calc='$calc'
  #end if
  #if int($abund.__str__) > 0:
   --abund=$abund
  #end if
  #if int($iters.__str__) > 0:
   --iters=$iters
  #end if
  #if float($freq.__str__) > 0:
   --freq=$freq
  #end if
  --processors=8
 </command>
 <inputs>
  <param name="otu" type="data" format="list,rabund,sabund,shared" label="list,rabund,sabund,shared - OTU List"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options>
    <filter type="data_meta" ref="otu" key="labels" />
   </options>
  </param>
  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
   <option value="ace">ace - Community richness the ACE estimator</option>
   <option value="bootstrap">bootstrap - Community richness the bootstrap estimator</option>
   <option value="chao">chao - Community richness the Chao1 estimator</option>
   <option value="jack">jack - Community richness the jackknife estimator</option>
   <option value="sobs" selected="true">sobs - Community richness the observed richness</option>
   <option value="simpsoneven">simpsoneven - Community evenness a Simpson index-based measure of evenness</option>
   <option value="shannoneven">shannoneven - Community evenness a Shannon index-based measure of evenness</option>
   <option value="heip">heip - Community evenness Heip's metric of community evenness</option>
   <option value="smithwilson">smithwilson - Community evenness Smith and Wilson's metric of community evenness</option>
   <option value="coverage">coverage - Community diversity the sampling coverage </option>
   <option value="simpson">simpson - Community diversity the Simpson index</option>
   <option value="invsimpson">invsimpson - Community diversity the Simpson index</option>
   <option value="shannon">shannon - Community diversity the Shannon index</option>
   <option value="npshannon">npshannon - Community diversity the non-parametric Shannon index</option>
   <option value="nseqs">nseqs - Utility the number of sequences in a sample</option>
  </param>
  <param name="abund" type="integer" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/>
  <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/>
  <param name="freq" type="float" value="0.0" label="freq - Reporting frequency" 
         help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/>
  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Create a new history dataset for each label and calculator"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
 </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.single_ command generates intra-sample rarefaction curves using a re-sampling without replacement approach. Rarefaction curves provide a way of comparing the richness observed in different samples.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators

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

 </help>
</tool>