<tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.16.0"  force_history_refresh="True">
 <description>Generate a heatmap for OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='heatmap.bin'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.heatmap\.bin\.svg)$:svg'
  --READ_cmd='read.otu'
  #if $input.source == 'similarity':
   --READ_list=$input.otu
   #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
    --READ_group='$otu_group'
   #end if
   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
    --READ_label='$input.label'
   #end if
  #elif $input.source == 'shared':
   --READ_relabund=$input.otu
   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
    --READ_label='$input.label'
   #end if
  #end if
  #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
   --groups=$input.groups
  #end if
  #if $scale.__str__ != "None" and len($scale.__str__) > 0:
   --scale='$scale'
  #end if
  #if $sorted.__str__ != "None" and len($sorted.__str__) > 0:
   --sorted='$sorted'
  #end if
  #if $numotu > 0:
   --numotu=$numotu
  #end if
  #if 100 > $fontsize > 0:
   --fontsize=$fontsize
  #end if
 </command>
 <inputs>
  <!-- get.relabund  relabund type should also work -->
 <conditional name="input">
   <param name="source" type="select" label="Generate Heatmap for">
    <option value="similarity">OTU list</option>
    <option value="relabund">OTU Relative Abundance</option>
   </param>
   <when value="similarity">
     <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/>
     <param name="otu_group" type="data" format="groups" label="read.otu(group) - Group file for the OTU List"/>
     <param name="label" type="select" label="label - OTU Labels" multiple="true">
      <options from_dataset="otu">
       <column name="name" index="0"/>
       <column name="value" index="0"/>
      </options>
     </param>
     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
      <options from_dataset="otu_group">
       <column name="name" index="1"/>
       <column name="value" index="1"/>
       <filter type="unique_value" name="unq_grp" column="1" />
      </options>
     </param>
   </when>
   <when value="relabund">
     <param name="otu" type="data" format="relabund" label="read.otu(relabund=) - OTU Relative Abundance"/>
     <param name="label" type="select" label="label - OTU Labels" multiple="true">
      <options from_dataset="otu">
       <column name="name" index="0"/>
       <column name="value" index="0"/>
      </options>
     </param>
     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
      <options from_dataset="otu">
       <column name="name" index="1"/>
       <column name="value" index="1"/>
       <filter type="unique_value" name="unq_grp" column="1" />
      </options>
     </param>
   </when>
  </conditional>
  <param name="scale" type="select" label="scale - Scaling for heatmap">
   <option value="">Default</option>
   <option value="log10">Log10</option>
   <option value="log2">Log2</option>
   <option value="linear">Linear</option>
  </param>
  <param name="sorted" type="select" label="sorted - Sort heatmap">
   <option value="">By shared</option>
   <option value="none">Don't sort</option>
   <option value="totalotu">By Total OTUs</option>
   <option value="totalgroup">By Total Groups</option>
  </param>
  <param name="numotu" type="integer" value="0" label="numotu - Limit the number of OTUs displayed (ignored if 0)"/>
  <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/>
 </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 heatmap.bin_ command generates a heat map from data provided in either a .list or a .shared file.

.. _heatmap.bin: http://www.mothur.org/wiki/Heatmap.bin

 </help>
</tool>