--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_otu_heatmap_html.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,57 @@
+<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>
+