--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alpha_diversity.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,112 @@
+<tool id="qiime_alpha_diversity" name="Calculate alpha diversity" version="1.9.1">
+    <description>on each sample in an otu table</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <version_command><![CDATA[
+        alpha_diversity.py --version
+    ]]>
+    </version_command>
+
+    <command>
+<![CDATA[
+        #set $chosen_metrics = str( $metrics ).split( "," )
+
+        alpha_diversity.py 
+            -i $input_table 
+            -o $alpha_diversity
+
+            -m $metrics
+
+            #if "PD_whole_tree" in $chosen_metrics:
+                -t $tree_file
+            #end if
+
+]]>
+    </command>
+
+    <inputs>
+        <param name="input_table" type="data" format="tabular,txt,tsv,biom" 
+            label="OTU table" help="(-i/--input_path)" 
+            multiple="True"/>
+
+        <param name="metrics" type="select" multiple="True" label="Alpha-diversity 
+            metric(s) to use" help="(-m/--metrics)" 
+            display="checkboxes">
+            <option value="ace">ACE (Abundance-based Coverage Estimator) metric</option>
+            <option value="berger_parker_d">Berger-Parker dominance</option>
+            <option value="brillouin_d">Brillouin index of alpha diversity</option>
+            <option value="chao1" selected="true">chao1 richness estimator</option>
+            <option value="chao1_ci">chao1 confidence interval</option>
+            <option value="dominance">Dominance</option>
+            <option value="doubles">Number of double occurrences (doubletons)</option>
+            <option value="enspie">ENS_pie alpha diversity measure</option>
+            <option value="equitability">Equitability</option>
+            <option value="esty_ci">Esty’s CI</option>
+            <option value="fisher_alpha">Fisher’s alpha</option>
+            <option value="gini_index">Gini index</option>
+            <option value="goods_coverage">Good’s coverage of counts</option>
+            <option value="heip_e">Heip’s evenness measure</option>
+            <option value="kempton_taylor_q">Kempton-Taylor Q index of alpha diversity</option>
+            <option value="margalef">Margalef’s richness index</option>
+            <option value="mcintosh_d">McIntosh dominance index D</option>
+            <option value="mcintosh_e">McIntosh’s evenness measure E</option>
+            <option value="menhinick">Menhinick’s richness index</option>
+            <option value="michaelis_menten_fit">Michaelis-Menten fit to rarefaction curve of observed OTUs</option>
+            <option value="observed_otus">Number of distinct OTUs</option>
+            <option value="observed_species" selected="true">Number of distinct species</option>
+            <option value="osd">Observed OTUs, singles, and doubles</option>
+            <option value="simpson_reciprocal">simpson_reciprocal</option>
+            <option value="robbins">Robbins’ estimator for the probability of unobserved outcomes</option>
+            <option value="shannon">Shannon entropy of counts</option>
+            <option value="simpson">Simpson’s index</option>
+            <option value="simpson_e">Simpson’s evenness measure E</option>
+            <option value="singles">Number of single occurrencesles</option>
+            <option value="strong"> Strong’s dominance index</option>
+            <option value="PD_whole_tree">Phylogenetic diversity</option>
+        </param>
+        
+        <param  name="tree_file" type="data" label="Newick tree (optional, except
+            for PD_whole_tree metric" help="(-t/--tree_path)" optional="True"/>
+    </inputs>
+
+    <outputs>
+        <data name="alpha_diversity" format="tabular" 
+            from_work_dir="alpha_diversity/alpha_div.txt" 
+            label="${tool.name} on ${on_string}: Alpha diversity" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_table" value="pick_open_reference_otus_otu_table.txt"/>
+            <param name="metrics" value="chao1,observed_species" />
+            <output name="alpha_diversity" value="" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**What it does?**
+
+This tool calculates alpha diversity, or within-sample diversity, using an
+OTU table.
+
+The resulting file(s) is a tab-delimited text file, where the columns correspond 
+to alpha diversity metrics and the rows correspond to samples and their calculated 
+diversity measurements. When a folder is given as input (-i), the script processes 
+every otu table file in the given folder, and creates a corresponding file in the 
+output directory.
+
+More information about this tool is available on 
+`QIIME documentation <http://qiime.org/scripts/alpha_diversity.html>`_.
+    ]]>
+    </help>
+
+    <citations>
+        <expand macro="citations" />
+    </citations>
+</tool>