<tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.15.0"  force_history_refresh="True">
 <description>Generate a heatmap for pariwise similarity</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='heatmap.sim'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.heatmap\.sim\.svg)$:svg'
  #if $input.source == 'similarity':
   --READ_cmd='read.otu'
   --READ_list=$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:
    --label='$input.label'
   #end if
   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
    --groups=$input.groups
   #end if
   #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0:
     --calc='$input.calc'
   #end if
  #elif $input.source == 'shared':
   --READ_cmd='read.otu'
   --READ_shared=$input.otu
   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
    --label='$input.label'
   #end if
   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
    --groups=$input.groups
   #end if
   #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0:
     --calc='$input.calc'
   #end if
  #elif $input.source == 'column':
   --column=$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
 </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="shared">OTU Shared</option>
    <option value="column">Pairwise Column Distance Matrix</option>
    <option value="phylip">Phylip Distance Matrix</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 include" 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>
     <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
      <options from_file="mothur_calulators.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>
   </when>
   <when value="shared">
    <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
    <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 include" 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>
   <when value="column">
       <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
       <param name="name" type="data" format="names" label="name - Names"/>
   </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>
  </conditional>
 </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.sim_ command generates a heat map from data provided in either a .list or a .shared file.

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

 </help>
</tool>