annotate mothur/tools/mothur/collect.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_collect_shared" name="Collect.shared" version="1.23.0" force_history_refresh="True">
 <description>Generate collector's curves for calculators on OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='collect.shared'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+?\.(anderberg|braycurtis|jabund|jclass|jest|kstest|kulczynski|kulczynskicody|lennon|morisitahorn|ochiai|shared\.ace|shared\.chao|shared\.nseqs|shared\.sobs|sorabund|sorclass|sorest|thetan|thetayc|whittaker)$:tabular'
  --shared=$otu
  #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
  $all
  #if float($freq.__str__) > 0:
   --freq=$freq
  #end if
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
   --groups=$groups
  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
  <param name="label" type="select" label="label - OTU Label filter" multiple="true">
   <help>To filter: select labels to include</help>
   <options>
    <filter type="data_meta" ref="otu" key="labels" />
   </options>
  </param>
  <param name="groups" type="select" label="groups - Groups filter (uses all groups if none are selected)" multiple="true">
   <help>To filter: select select at least 2 groups</help>
   <options>
    <filter type="data_meta" ref="otu" key="groups" />
   </options>
  </param>
  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none are 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="freq" type="float" value="0.0" label="freq - "/>
  <param name="all" type="boolean" truevalue="--all=true" falsevalue="" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/>
 </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.shared_ command generates collector's curves for calculators_, which describe the similarity between communities or their shared richness. 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.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators

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

 </help>
</tool>