annotate mothur/tools/mothur/venn.xml @ 27:49058b1f8d3f

Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur

<tool id="mothur_venn" name="Venn" version="1.23.0"  force_history_refresh="True">
 <description>Generate Venn diagrams for groups </description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='venn'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  #if $as_datasets.__str__ == "yes":
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.(\S+\.svg)$:svg'
  #end if
  #if $input.source == 'shared':
   --shared=$input.otu
   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
    --label='$input.label'
   #end if
   #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0:
     --calc='$input.calc'
   #end if
   $nseqs
   $permute
   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
    --groups=$input.groups
   #end if
  #elif $input.source == 'similarity':
   --list=$input.otu
   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
    --label='$input.label'
   #end if
   #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0:
     --calc='$input.calc'
   #end if
   #if $input.abund >= 5:
     --abund='$input.abund'
   #end if
  #end if
  #if 100 > $fontsize > 0:
   --fontsize=$fontsize
  #end if
 </command>
 <inputs>
  <conditional name="input">
   <param name="source" type="select" label="Generate Heatmap for">
    <option value="shared">OTU Shared</option>
    <option value="similarity">OTU list</option>
   </param>
   <when value="shared">
     <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
     <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
      <option value="sharedsobs">Shared Sobs</option>
      <option value="sharedchao">Shared Chao</option>
      <option value="sharedace">Shared Ace</option>
     </param>
     <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 consider" multiple="true">
      <options>
       <filter type="data_meta" ref="otu" key="groups" />
      </options>
     </param>
   </when>
   <when value="similarity">
     <param name="otu" type="data" format="list" label="list - OTU List"/>
     <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
      <option value="sobs">Sobs</option>
      <option value="chao">Chao</option>
      <option value="ace">Ace</option>
     </param>
     <param name="abund" type="integer" value="10" label="abund - Abundance when using the ace calculator ( >= 5 )">
      <validator type="in_range" min="5" />
     </param>
     <param name="label" type="select" label="label - OTU Labels" multiple="true">
      <options>
       <filter type="data_meta" ref="otu" key="labels" />
      </options>
     </param>
   </when>
  </conditional>
  <param name="nseqs" type="boolean" truevalue="--nseqs=true" falsevalue="" checked="false" label="nseqs - Output the number of sequences represented by the otus in the picture"/>
  <param name="permute" type="boolean" truevalue="--permute=true" falsevalue="" checked="false" label="permute - Create pictures with all possible 4-way permutations of groups"/>
  <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/>
  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">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 venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators

.. _venn: http://www.mothur.org/wiki/Venn

 </help>
</tool>