--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alpha_rarefaction.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,117 @@
+<tool id="qiime_alpha_rarefaction" name="Perform alpha rarefaction" version="1.9.1">
+
+    <description></description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <version_command><![CDATA[
+        alpha_rarefaction.py --version
+    ]]>
+    </version_command>
+
+    <command>
+<![CDATA[        
+    alpha_rarefaction.py 
+        -i $otu_table_fp 
+        -m $mapping_fp
+        -o alpha_rarefaction
+
+        #if $parameter_fp
+            -p $parameter_fp
+        #end if
+
+        -n $num_steps
+        $parallel
+        -O "\${GALAXY_SLOTS:-4}"
+
+        #if $tree_fp
+            -t $tree_fp
+        #end if
+
+        --min_rare_depth $min_rare_depth
+
+        #if $max_rare_depth
+            -e $max_rare_depth
+        #end if
+
+        &&
+        mkdir -p $alpha_rarefaction_plots.files_path 
+        &&
+        cp -r alpha_rarefaction/alpha_rarefaction_plots/rarefaction_plots.html $alpha_rarefaction_plots.files_path  
+        &&
+        cp -r alpha_rarefaction/alpha_rarefaction_plots/average_plots $alpha_rarefaction_plots.files_path  
+        &&
+        mv $alpha_rarefaction_plots.files_path/rarefaction_plots.html $alpha_rarefaction_plots
+]]>
+    </command>
+
+    <inputs>
+        <param name="otu_table_fp" type="data" format="tabular,txt,tsv,biom" 
+            label="OTU table" help="(-i/--otu_table_fp)" />
+
+        <param name="mapping_fp" type="data" format="tabular,txt,tsv" 
+            label="Mapping file" help="(-m/--mapping_fp)" />
+
+        <param name="parameter_fp" type="data" format="txt" 
+            label="Parameter file" help="It specifies changes to the default 
+            behavior (-p/--parameter_fp)" optional="true"/>
+
+        <param name="num_steps" type="integer" value="10" label="Number of steps 
+            (or rarefied OTU table sizes) to make between min and max counts" 
+            help="(-n/--num_steps)"/>
+
+        <param name="parallel" type="boolean" label="Run in parallel where 
+            available?" truevalue="--parallel" falsevalue="" checked="True" 
+            help="(-a, --parallel)" />
+
+        <param name="tree_fp" type="data" format="tabular,txt,tsv" 
+            label="Tree file (optional)" help="Required for phylogenetic measures 
+            (-t/--tree_fp)" optional="True"/>
+
+        <param name="min_rare_depth" type="integer" value="10" label="Lower limit 
+            of rarefaction depths" help="(--min_rare_depth)"/>
+
+        <param name="max_rare_depth" type="integer" label="Upper limit 
+            of rarefaction depths" help="By default, median sequence/sample count
+            is used (-e/--max_rare_depth)" optional="True"/>
+    </inputs>
+
+    <outputs>
+        <data name="alpha_rarefaction_plots" format="html" 
+            label="${tool.name} on ${on_string}: Alpha rarefaction plots"/>
+
+        <data format="txt" name="alpha_diversity">
+            <discover_datasets pattern="__designation__" ext="txt" 
+                directory="alpha_rarefaction/alpha_div_collated" visible="true" />
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**What it does**
+
+This script performs alpha rarefaction in several steps:
+
+    - Generation of rarefied OTU tables
+    - Computation of alpha diversity metrics for each rarefied OTU table
+    - Concatenation of alpha diversity results
+    - Generation of alpha rarefaction plots
+
+More information about this tool is available on 
+`QIIME documentation <http://qiime.org/scripts/alpha_rarefaction.html>`_.
+    ]]>
+    </help>
+
+    <citations>
+        <expand macro="citations" />
+    </citations>
+</tool>