annotate mothur/tools/mothur/heatmap.bin.xml @ 27:49058b1f8d3f

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

<tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.20.0"  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'
  #if $as_datasets.__str__ == "yes":
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.heatmap\.bin\.svg)$:svg'
  #end if
  #if isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
   --shared=$input.otu
  #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
   --rabund=$input.otu
  #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__):
   --sabund=$input.otu
  #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__):
   --list=$input.otu
  #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__):
   --relabund=$input.otu
  #end if
  #if $input.has_groups != 'no' and $input.groups.__str__ != "None" and len($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
  #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>
  <conditional name="input">
   <param name="has_groups" type="select" label="Generate Heatmap for">
    <option value="default">shared  or relabund</option>
    <option value="no">list, rabund, sabund</option>
    <option value="yes">list, rabund, sabund with groups</option>
   </param>
   <when value="default">
     <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU List"/>
     <param name="groups" type="select" label="groups - Groups to condider" multiple="true">
      <options>
       <filter type="data_meta" ref="otu" key="groups" />
      </options>
     </param>
     <param name="label" type="select" label="label - OTU Labels" multiple="true">
      <options>
       <filter type="data_meta" ref="otu" key="labels" />
      </options>
     </param>
   </when>
   <when value="no">
     <param name="otu" type="data" format="list,rabund,sabund" label="list,rabund,sabund - OTU List"/>
     <param name="label" type="select" label="label - OTU Labels" multiple="true">
      <options>
       <filter type="data_meta" ref="otu" key="labels" />
      </options>
     </param>
   </when>
   <when value="yes">
     <param name="otu" type="data" format="list,rabund,sabund" label="list,rabund,sabund - OTU List"/>
     <param name="otu_group" type="data" format="groups" label="group - Group file for the OTU List"/>
     <param name="groups" type="select" label="groups - Groups to include" multiple="true">
      <options>
       <filter type="data_meta" ref="otu_group" key="groups" />
      </options>
     </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="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="topotu">By Total OTUs</option>
   <option value="topgroup">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)"/>
  <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 heatmap.bin_ command generates a heat map from data provided in either a list_ or a shared_ file.

.. _list: http://www.mothur.org/wiki/List_file
.. _shared: http://www.mothur.org/wiki/Shared_file
.. _heatmap.bin: http://www.mothur.org/wiki/Heatmap.bin

 </help>
</tool>