--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core_diversity_analyses.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,143 @@
+<tool id="qiime_core_diversity" name="Compute core set of diversity analyses" version="1.9.1">
+    <description></description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <version_command><![CDATA[
+        core_diversity_analyses.py --version
+    ]]>
+    </version_command>
+
+    <command>
+<![CDATA[
+        core_diversity_analyses.py 
+            -i $input_biom_fp 
+            -o core_diversity_analyses
+            -m $mapping_fp
+            -e $sampling_depth
+
+            #if $parameter_fp
+                -p $parameter_fp
+            #end if
+
+            $parallel
+            -O "\${GALAXY_SLOTS:-4}"
+
+            #if $phylogenetic.nonphylogenetic_diversity
+                --nonphylogenetic_diversity
+            #else
+                -t $phylogenetic.tree_fp
+            #end if
+
+            $suppress_taxa_summary
+            $suppress_beta_diversity
+            $suppress_alpha_diversity
+            $suppress_group_significance
+
+            #if $categories
+                -c $categories
+            #end if
+
+        &&
+        mkdir -p $html_report.files_path 
+        &&
+        cp -r core_diversity_analyses/* $html_report.files_path  
+        && 
+        mv $html_report.files_path/index.html $html_report
+]]>
+    </command>
+
+    <inputs>
+        <param name="input_biom_fp" type="data" format="tabular,txt,tsv,biom" 
+            label="OTU table" help="(-i/--input_biom_fp)"/>
+
+        <param name="mapping_fp" type="data" format="tabular,txt,tsv" 
+            label="Mapping file" help="(-m/--mapping_fp)"/>
+
+        <param name="sampling_depth" type="integer" value="" label="Sequencing 
+            depth to use for even sub-sampling and maximum rarefaction depth" 
+            help="To decide this value, review the output of the 
+            ‘biom summarize-table’ (-e/--sampling_depth)"/>
+
+        <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="parallel" type="boolean" label="Run in parallel where 
+            available?" truevalue="--parallel" falsevalue="" checked="true" 
+            help="(-a, --parallel)" />
+
+        <conditional name="phylogenetic">
+            <param name="nonphylogenetic_diversity" type="boolean" label="Apply 
+                non-phylogenetic alpha (chao1 and observed_otus) and beta (bray_curtis) 
+                diversity calculations?" truevalue="--nonphylogenetic_diversity" 
+                falsevalue="" checked="false" help="This is useful if, for example, 
+                when working with non-amplicon BIOM tables, or if a reliable tree 
+                is not available (--nonphylogenetic_diversity)" /> 
+            <when value="false" >
+                <param name="tree_fp" type="data" format="txt" 
+                    label="Tree file" help="(-t/--tree_fp)"/>
+            </when>
+            <when value="true" />
+        </conditional>
+
+        <param name="suppress_taxa_summary" type="boolean" label="Suppress 
+            generation of taxa summary plots?" truevalue="--suppress_taxa_summary" 
+            falsevalue="" checked="False" help="(--suppress_taxa_summary)" /> 
+
+        <param name="suppress_beta_diversity" type="boolean" label="Suppress 
+            beta diversity analyses?" truevalue="--suppress_beta_diversity" 
+            falsevalue="" checked="False" help="(--suppress_beta_diversity)" /> 
+
+        <param name="suppress_alpha_diversity" type="boolean" label="Suppress 
+            alpha diversity analyses?" truevalue="--suppress_alpha_diversity" 
+            falsevalue="" checked="False" help="(--suppress_alpha_diversity)" />
+
+        <param name="suppress_group_significance" type="boolean" label="Suppress 
+            OTU/category significance analysis?" truevalue="--suppress_group_significance" 
+            falsevalue="" checked="False" help="(--suppress_group_significance)" /> 
+
+        <param name="categories" type="text" value="" label="Metadata category or 
+            categories to compare for categorical analyses (optional)" 
+            help="The column headers in the mapping file should be passed as a 
+            comma-separated list. By default, no categorical analyses are performed
+            (-c/--categories)" optional="true"/>
+
+    </inputs>
+
+    <outputs>
+        <data name="html_report" format="html" 
+            label="${tool.name} on ${on_string}: Core diversity report" />
+    </outputs>
+
+    <tests>
+        <test>
+        </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>