<tool id="make_otu_heatmap_html" name="make_otu_heatmap_html" version="1.2.1">
 <description>Make heatmap of OTU table</description>
 <requirements>
  <requirement type="binary">make_otu_heatmap_html.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_outputdir='$otu_heatmp.extra_files_path'
  --galaxy_datasets='^\S+\.html$:'$otu_heatmp
  make_otu_heatmap_html.py
  --otu_table_fp=$otu_table_fp
  --output_dir='$otu_heatmp.extra_files_path'
  --num_otu_hits=$num_otu_hits
  #if $tree != None and $tree.__str__ != 'None':
   --tree=$tree
  #end if
  #if $map_fname != None and $map_fname.__str__ != 'None' > 0:
   --map_fname=$map_fname
  #end if
  #if $sample_tree != None and $sample_tree.__str__ != 'None':
   --sample_tree=$sample_tree
  #end if
  $log_transform
  --log_eps=$log_eps
 </command>
 <inputs>
  <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
   help="path to the input OTU table (i.e., the output from make_otu_table.py) [REQUIRED]"/>
  <param name="num_otu_hits" type="integer" value="5" label="num_otu_hits"
   help="This is the minimum number of Samples that an OTU is present in, for an OTU to be kept in the OTU table [default: 5]"/>
  <param name="tree" type="data" format="tre"  optional="true" label="tree"
   help="Tree file to be used for sorting OTUs in the heatmap"/>
  <param name="map_fname" type="data" format="qiimemapping" optional="true" label="map_fname"
   help="Metadata mapping file to be used for sorting Samples in the heatmap"/>
  <param name="sample_tree" type="data" format="tre"  optional="true" label="sample_tree"
   help="Tree file to be used for sorting samples (e.g, output from upgma_cluster.py). If both this and the sample mapping file are provided, the mapping file is ignored."/>
  <param name="log_transform" type="boolean" truevalue="--log_transform" falsevalue="" checked="false" label="log_transform"
   help="Data will be log-transformed. All zeros will be set to a small value (default is 1/2 the smallest non-zero entry). Data will be translated to be non-negative after log transform, and num_otu_hits will be set to 0."/>
  <param name="log_eps" type="float" value="0.0" label="log_eps"
   help="Small value to replace zeros for log transform. [default: 1/2 the smallest non-zero entry]."/>
 </inputs>
 <outputs>
    <!-- TODO 
     the html output has a js sub dir:
       move the js/* to the html .extra_files_path/
       filter the html to remove 'js/' sub dir
     -->
   <data name="otu_heatmp" format="html" label="${tool.name} on ${on_string}: otu_heatmp"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
  
 </help>
</tool>