annotate mothur/tools/mothur/collect.single.xml @ 25:bfbaf823be4c

Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.

<tool id="mothur_collect_single" name="Collect.single" version="1.20.0" force_history_refresh="True">
 <description>Generate collector's curves for OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='collect.single'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  #if $as_datasets.__str__ == 'yes':
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.(\S+)$: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=$abund
  #end if
  #if int($size.__str__) > 0:
   --size=$size
  #end if
  #if float($freq.__str__) > 0:
   --freq=$freq
  #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 (default 10)"/>
  <param name="size" type="integer" value="0" label="size - sample size for OTU prediction (ignored if &lt; 1)" 
    help="By default these calculators will base the prediction on a sample that is the same size as the initial sampling"/>
  <param name="freq" type="float" value="0.0" label="freq - frequency for output (default is every 100 sequences)" 
    help="Use a decimal between 0 and 1 to set the frequency as a percentage of the number of sequences"/>
  <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="binary">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 collect.single_ command generates collector's curves using calculators_, that describe the richness, diversity, and other features of individual samples. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. Otherwise, you need to keep sampling.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators

.. _calculators: http://www.mothur.org/wiki/Calculators
.. _collect.single: http://www.mothur.org/wiki/Collect.single

 </help>
</tool>