annotate mothur/tools/mothur/tree.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_tree_shared" name="Tree.shared" version="1.23.0" force_history_refresh="True">
 <description>Generate a newick tree for dissimilarity among groups</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='tree.shared'
  #if $input.source == 'shared':
   --result='^mothur.\S+\.logfile$:'$logfile
   #if $input.as_datasets.__str__ == "yes":
    --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
    --new_datasets='^\S+?([a-z]+\.(unique|[0-9.]*)\.tre)$:tre'
   #end if
   --shared=$input.dist
   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
    --groups=$input.groups
   #end if
   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
    --label='$input.label'
   #end if
  #else: 
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tre$:'$tre
   --outputdir='$logfile.extra_files_path'
   #if $input.source == 'column':
    --column=$input.dist
    --name=$input.name
   #elif $input.source == 'phylip':
    --phylip=$input.dist
    #if $input.name.__str__ != "None" and len($input.name.__str__) > 0:
     --name=$input.name
    #end if
   #end if
  #end if
  #if $calc.__str__ != "None" and len($calc.__str__) > 0:
   --calc=$calc
  #end if
 </command>
 <inputs>
  <!-- column,name  phylip  or shared -->
  <conditional name="input">
   <param name="source" type="select" label="Select input format">
    <option value="shared">OTU Shared</option>
    <option value="column">Pairwise Column Distance Matrix</option>
    <option value="phylip">Phylip Distance Matrix</option>
   </param>
   <when value="column">
    <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
    <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
   </when>
   <when value="phylip">
    <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
    <param name="name" type="data" format="names" optional="true" label="name - Names"/>
   </when>
   <when value="shared">
     <param name="dist" type="data" format="shared" label="shared - OTU Shared"/>
     <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label and calculator"/>
     <param name="label" type="select" label="label - OTU Labels" multiple="true">
      <options>
       <filter type="data_meta" ref="dist" key="labels" />
      </options>
     </param>
     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
      <options>
       <filter type="data_meta" ref="dist" key="groups" />
      </options>
     </param>
   </when>
  </conditional>
  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
   <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
   <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
   <option value="sharedace">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">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">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
   <option value="sorest">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">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">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
   <option value="thetan">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>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tre" name="tre" label="${tool.name} on ${on_string}: tre">
   <filter>input['source'] != 'shared'</filter>
  </data>
 </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 tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators

.. _tree.shared: http://www.mothur.org/wiki/Tree.shared


 </help>
</tool>