--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alpha_diversity.xml	Thu May 18 09:32:36 2017 -0400
@@ -0,0 +1,94 @@
+<tool id="qiime_alpha_diversity" name="Calculate alpha diversity" version="@WRAPPER_VERSION@.0">
+    <description>on each sample in an otu table</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <version_command>alpha_diversity.py --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        #set $chosen_metrics = str( $metrics ).split( "," )
+        alpha_diversity.py
+            --input_path '$input_path'
+            -o alphadiv
+            --metrics '$metrics'
+            #if "PD_whole_tree" in $chosen_metrics:
+                --tree_path '$tree_path'
+            #end if
+    ]]></command>
+    <inputs>
+        <param argument="--input_path" type="data" format="tabular,txt,tsv,biom" multiple="True"  label="OTU table"/>
+        <param argument="--metrics" type="select" multiple="True"  display="checkboxes" label="Alpha-diversity metric(s) to use">
+            <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 argument="--tree_path" type="data" format="nhx" optional="True"  label="Newick tree (optional, except for PD_whole_tree metric)"/>
+    </inputs>
+    <outputs>
+        <data name="alpha_diversity" format="tabular" from_work_dir="alphadiv" label="${tool.name} on ${on_string}: Alpha diversity"/>
+    </outputs>
+    <tests>
+        <test><!-- test with defaults -->
+            <param name="input_path" value="alpha_diversity/otu_table.biom"/>
+            <output name="alpha_diversity" file="alpha_diversity/alphadiv"/>
+        </test>
+        <test><!-- test with all metrics and tree file -->
+            <param name="input_path" value="alpha_diversity/otu_table.biom"/>
+            <param name="metrics" value="ace,berger_parker_d,brillouin_d,chao1,chao1_ci,dominance,doubles,enspie,equitability,esty_ci,fisher_alpha,gini_index,goods_coverage,heip_e,kempton_taylor_q,margalef,mcintosh_d,mcintosh_e,menhinick,michaelis_menten_fit,observed_otus,observed_species,osd,simpson_reciprocal,robbins,shannon,simpson,simpson_e,singles,strong,PD_whole_tree"/>
+            <param name="tree_path" value="alpha_diversity/rep_set.tre"/>
+            <output name="alpha_diversity" ftype="tabular">
+                <assert_contents>
+                    <has_text text="ace"/>
+                    <has_text text="simpson"/>
+                    <has_text text="PD_whole_tree"/>
+                </assert_contents>
+            </output>
+        </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>