<tool id="mothur_summary_single" name="Summary.single" version="1.19.0" force_history_refresh="True">
 <description>Summary of calculator values for OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='summary.single'
  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__) and not $groupmode.__str__ == '--groupmode=true': 
   --result='^mothur.\S+\.logfile$:'$logfile
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+\.((\S+?)\.summary)$:tabular'
  #else:
   #if $subsample.use.__str__ == 'yes':
    --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.groups\.ave-std\.summary$:'$subsample_summary,'^\S+\.groups\.summary$:'$summary,
   #else
    --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary
   #end if
  #end if
  --outputdir='$logfile.extra_files_path'
  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
   --shared=$otu
   $groupmode
  #elif isinstance($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=$abund
  #end if
  #if int($size.__str__) > 0:
   --size=$size
  #end if
  #if $subsample.use.__str__ == 'yes':
   #if $subsample.subsample.__str__ != '':
     --subsample=$subsample.subsample
   #else
     --subsample=T
   #end if
   #if $subsample.iters.__str__ != '':
     --iters=$subsample.iters
   #end if
  #end if
 </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" selected="true">ace - Community richness the ACE estimator</option>
   <option value="bootstrap">bootstrap - Community richness the bootstrap estimator</option>
   <option value="chao" selected="true">chao - Community richness the Chao1 estimator</option>
   <option value="jack" selected="true">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="bergerparker">bergerparker - Community diversity the Berger-Parker index</option>
   <option value="coverage">coverage - Community diversity the sampling coverage </option>
   <option value="goodscoverage">goodscoverage - Community diversity the Good's estimate of sampling coverage </option>
   <option value="simpson" selected="true">simpson - Community diversity the Simpson index</option>
   <option value="invsimpson">invsimpson - Community diversity the Simpson index</option>
   <option value="qstat">qstat - Community diversity the Q statistic</option>
   <option value="shannon" selected="true">shannon - Community diversity the Shannon index</option>
   <option value="npshannon" selected="true">npshannon - Community diversity the non-parametric Shannon index</option>
   <option value="boneh">boneh - Estimator Boneh's estimator</option>
   <option value="efron">efron - Estimator Efron's estimator</option>
   <option value="shen">shen - Estimator Shen's estimator</option>
   <option value="solow">solow - Estimator Solow's estimator</option>
   <option value="logseries">logseries - Statistical distribution tests whether observed data follow the log series distribution</option>
   <option value="geometric">geometric - Statistical distribution tests whether observed data follow the geometric series distribution</option>
   <option value="bstick">bstick - Statistical distribution tests whether observed data follow the broken stick distribution</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="size" type="integer" value="0" label="size - "/>
  <conditional name="subsample">
    <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="produce subsample distance matrices"/>
    <when value="yes">
      <param name="subsample" type="integer" value="" optional="true" label="subsample - size of the sample" 
             help="If using shared input: may be left blank to use the size of your smallest group"/>
      <param name="iters" type="integer" value="0" optional="true" label="iters - Number of times to run the subsample"/>
    </when>
    <when value="no"/>
  </conditional>
  <param name="groupmode" type="boolean" truevalue="--groupmode=true" falsevalue="--groupmode=false" checked="true" 
    label="groupmode - Collate shared summary results in one file"
    help="If false, create a summary file per group."/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary" >
   <filter>(otu.file_ext == 'shared' and groupmode == True)</filter>
  </data>
  <data format="tabular" name="subsample_summary" label="${tool.name} on ${on_string}: ave-std.summary" >
   <filter>(subsample['use'] and not (otu.file_ext == 'shared' and groupmode == False))</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 summary.single_ command produce a summary file that has the calculator value for each line in the OTU data and for all possible comparisons between the different groups in the group_ file.  This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators

.. _group: http://www.mothur.org/wiki/Group_file
.. _summary.single: http://www.mothur.org/wiki/Summary.single

 </help>
</tool>