annotate mothur/tools/mothur/rarefaction.shared.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_rarefaction_shared" name="Rarefaction.shared" version="1.20.0">
 <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=$groups
  #end if
  #if int($iters.__str__) > 0:
   --iters=$iters
  #end if
  $jumble
  #if $calc.__str__ != "None" and len($calc.__str__) > 0:
    --calc='$calc'
  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options>
    <filter type="data_meta" ref="otu" key="labels" />
   </options>
  </param>
  <param name="groups" type="select" label="groups - Groups to analyze" multiple="true">
   <help>All groups will be analyzed by default if none are selected</help>
   <options>
    <filter type="data_meta" ref="otu" key="groups" />
    <filter type="add_value" name="all" value="all" />
   </options>
  </param>
  <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/>
  <param name="jumble" type="boolean" truevalue="" falsevalue="--jumble=false" checked="true" label="jumble"/>
  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
   <option value="sharedobserved" selected="true">sharedobserved - the number of sequences in two samples</option>
   <option value="sharednseqs">sharednseqs - the number of sequences in two samples</option>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction" />
 </outputs>
 <requirements>
  <requirement type="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 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>