annotate mothur/tools/mothur/tree.shared.xml @ 15:a6189f58fedb

Mothur - updated for Mothur version 1.22.0

<tool id="mothur_tree_shared" name="Tree.shared" version="1.20.0" 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 from_dataset="dist">
       <column name="name" index="0"/>
       <column name="value" index="0"/>
       <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/>
       <filter type="unique_value" name="unq_lbl" column="0" />
      </options>
     </param>
     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
      <options from_dataset="dist">
       <column name="name" index="1"/>
       <column name="value" index="1"/>
       <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/>
       <filter type="unique_value" name="unq_grp" column="1" />
      </options>
     </param>
   </when>
  </conditional>
  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
   <options from_file="mothur_calculators.loc">
     <column name="mult2" index="2"/>
     <column name="name" index="0"/>
     <column name="value" index="0"/>
     <filter type="static_value" name="mult2" column="2" value="shar" />
   </options>
  </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>