view mothur/tools/mothur/summary.shared.xml @ 36:040410b8167e default tip

Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.

<tool id="mothur_summary_shared" name="Summary.shared" version="1.27.0"  force_history_refresh="True">
 <description>Summary of calculator values for OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='summary.shared'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --shared=$otu
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
   --groups=$groups
  #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
  $all
  $distance
  #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
   #if len($subsample.output.__str__) > 0:
    --output=$subsample.output
   #end if
   #if $subsample.as_datasets.__str__ == 'yes':
    --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
    #if $subsample.output.__str__ == 'square':
     ## patient70.fn.jest.0.16.lt.ave.dist
     --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)(\.(ave|std))?\.dist)$:square.dist'
    #else
     ## patient70.fn.jest.0.13.square.std.dist
     --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)(\.(ave|std))?\.dist)$:lower.dist'
    #end if
   #end if
  #end if
  --processors=8
 </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 - Pairwise comparision groups" multiple="true">
   <options>
    <filter type="data_meta" ref="otu" key="groups" />
   </options>
  </param>
  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
   <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
   <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
   <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
   <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
   <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
   <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
   <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
   <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
   <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
   <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
   <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
   <option value="sorclass" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
   <option value="sorest" selected="true">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
   <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
   <option value="hamming">hamming - Community Membership Similarity -</option>
   <option value="memchi2">memchi2 - Community Membership Similarity -</option>
   <option value="memchord">memchord - Community Membership Similarity -</option>
   <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
   <option value="mempearson">mempearson - Community Membership Similarity -</option>
   <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
   <option value="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
   <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
   <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
   <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
   <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
   <option value="canberra">canberra - Community Structure Similarity -</option>
   <option value="gower">gower - Community Structure Similarity -</option>
   <option value="hellinger">hellinger - Community Structure Similarity -</option>
   <option value="manhattan">manhattan - Community Structure Similarity -</option>
   <option value="odum">odum - Community Structure Similarity -</option>
   <option value="soergel">soergel - Community Structure Similarity -</option>
   <option value="spearman">spearman - Community Structure Similarity -</option>
   <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
   <option value="structchi2">structchi2 - Community Structure Similarity -</option>
   <option value="structchord">structchord - Community Structure Similarity -</option>
   <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
   <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
   <option value="structpearson">structpearson - Community Structure Similarity -</option>
   <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
   <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
  </param>
  <param name="all" type="boolean" truevalue="--all=true" falsevalue="" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/>
  <param name="distance" type="boolean" truevalue="--distance=true" falsevalue="" checked="false" label="distance - Output a distance file for each calculator at each label"/>

  <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 pergroup of the sample" 
             help="Leave 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"/>
    <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
     <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option>
     <option value="square">Phylip formatted Square Matrix</option>
    </param>
    <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each dataset"
           help="the marices can be viewed from links in the logfile"/>
  </conditional>
 </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}: shared.summary" />
 </outputs>
 <requirements>
  <requirement type="package" version="1.33">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.shared_ command produce a summary file that has the calculator value for each line in the OTU data of the shared_ file 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  

.. _shared: http://www.mothur.org/wiki/Shared_file
.. _group: http://www.mothur.org/wiki/Group_file
.. _summary.shared: http://www.mothur.org/wiki/Summary.shared

 </help>
</tool>