--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime/collate_alpha.xml	Wed Jun 06 16:40:30 2012 -0400
@@ -0,0 +1,38 @@
+<tool id="collate_alpha" name="collate_alpha" version="1.2.0">
+ <description>Collate alpha diversity results</description>
+ <requirements>
+  <requirement type="binary">collate_alpha.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_outputdir=$output1.extra_files_path
+  --galaxy_new_files_path='$__new_file_path__'
+  --galaxy_logfile=$output1
+  --galaxy_new_datasets='^\S+\.txt$:txt'
+  --galaxy_datasetid=$output1.id
+  collate_alpha.py
+  --input_path=$input_path.extra_files_path
+  --output_path='$__new_file_path__'
+ </command>
+ <inputs>
+  <param name="input_path" type="data" format="txt"  label="input_path"
+   help="Input is alpha diversity log file [REQUIRED]"/>
+  <!--<param name="example_path" type="text"  label="example_path"
+   help="example alpha_diversity analysis file, containing all samples and all metrics to be included in the collated result[Default: chosen automatically (see usage string)]"/>-->
+ </inputs>
+ <outputs>
+  <data format="txt" name="output1" label="${tool.name} on ${on_string}"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>This tool concatenates all the files generated by alpha_diversity in order to generate rarefaction curves. The input is therefore the log file generated by alpha_diversity, and the output is a log file listing all the output files, as well as the files themselves. Galaxy must be manually refreshed after running this tool to view all output files.
+ 
+For more information, see collate_alpha_ in the Qiime documentation.
+ 
+Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
+
+Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
+
+.. _collate_alpha: http://qiime.org/scripts/collate_alpha.html</help>
+</tool>
+