--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core_diversity_analyses.xml	Thu May 18 09:37:30 2017 -0400
@@ -0,0 +1,137 @@
+<tool id="qiime_core_diversity" name="Compute core set of diversity analyses" version="@WRAPPER_VERSION@.0">
+    <description>A workflow for running a core set of QIIME diversity analyses</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <version_command>core_diversity_analyses.py --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        ## set matplotlib backend
+        echo "backend:agg" > matplotlibrc &&
+
+        core_diversity_analyses.py
+            --input_biom_fp '$input_biom_fp'
+            -o core_diversity_analyses
+            --mapping_fp '$mapping_fp'
+            --sampling_depth '$sampling_depth'
+            #if $parameter_fp
+                --parameter_fp '$parameter_fp'
+            #end if
+            $parallel
+            -O "\${GALAXY_SLOTS:-4}"
+            $phylogenetic.nonphylogenetic_diversity
+            #if str( $phylogenetic.nonphylogenetic_diversity ) == ""
+                --tree_fp '$phylogenetic.tree_fp'
+            #end if
+            $suppress_taxa_summary
+            $suppress_beta_diversity
+            $suppress_alpha_diversity
+            $suppress_group_significance
+            #if str( $categories ):
+                --categories '$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 argument="--input_biom_fp" type="data" format="tabular,txt,biom,h5" label="OTU table"/>
+        <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file" />
+        <param argument="--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’"/>
+        <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior" optional="true"/>
+        <param argument="--parallel" type="boolean" label="Run in parallel where available?" truevalue="--parallel" falsevalue="" checked="true"/>
+        <conditional name="phylogenetic">
+            <param argument="--nonphylogenetic_diversity" type="select" label="Apply non-phylogenetic alpha (chao1 and observed_otus) and beta (bray_curtis) diversity calculations?" help="This is useful if, for example, when working with non-amplicon BIOM tables, or if a reliable tree is not available">
+                <option value="--nonphylogenetic_diversity">Yes</option>
+                <option value="" selected="true">No</option>
+            </param>
+            <when value="">
+                <param argument="--tree_fp" type="data" format="txt" label="Tree file"/>
+            </when>
+            <when value="--nonphylogenetic_diversity"/>
+        </conditional>
+        <param argument="--suppress_taxa_summary" type="boolean" label="Suppress generation of taxa summary plots?" truevalue="--suppress_taxa_summary" falsevalue="" checked="False"/>
+        <param argument="--suppress_beta_diversity" type="boolean" label="Suppress beta diversity analyses?" truevalue="--suppress_beta_diversity" falsevalue="" checked="False"/>
+        <param argument="--suppress_alpha_diversity" type="boolean" label="Suppress alpha diversity analyses?" truevalue="--suppress_alpha_diversity" falsevalue="" checked="False"/>
+        <param argument="--suppress_group_significance" type="boolean" label="Suppress OTU/category significance analysis?" truevalue="--suppress_group_significance" falsevalue="" checked="False"/>
+        <param argument="--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" optional="true"/>
+    </inputs>
+    <outputs>
+        <data name="html_report" format="html" label="${tool.name} on ${on_string}: Core diversity report"/>
+    </outputs>
+    <tests>
+        <test> <!-- test taxa summary and group significance -->
+            <param name="input_biom_fp" value="core_diversity_analyses/otu_table.biom"/>
+            <param name="mapping_fp" value="core_diversity_analyses/map.txt"/>
+            <param name="sampling_depth" value="22"/>
+            <param name="parallel" value="--parallel"/>
+            <param name="nonphylogenetic_diversity" value=""/>
+            <param name="tree_fp" value="core_diversity_analyses/rep_set.tre"/>
+            <param name="suppress_taxa_summary" value=""/>
+            <param name="suppress_beta_diversity" value="--suppress_beta_diversity"/>
+            <param name="suppress_alpha_diversity" value="--suppress_alpha_diversity"/>
+            <param name="suppress_group_significance" value=""/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Filtered BIOM table (minimum sequence count: 22)"/>
+                    <has_text text="rarefied BIOM table (sampling depth: 22)"/>
+                    <has_text text="Taxa summary bar plots"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test><!-- test beta diversity -->
+            <param name="input_biom_fp" value="core_diversity_analyses/otu_table.biom"/>
+            <param name="mapping_fp" value="core_diversity_analyses/map.txt"/>
+            <param name="sampling_depth" value="22"/>
+            <param name="parallel" value="--parallel"/>
+            <param name="nonphylogenetic_diversity" value="--nonphylogenetic_diversity"/>
+            <param name="suppress_taxa_summary" value="--suppress_taxa_summary"/>
+            <param name="suppress_beta_diversity" value=""/>
+            <param name="suppress_alpha_diversity" value="--suppress_alpha_diversity"/>
+            <param name="suppress_group_significance" value="--suppress_group_significance"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Filtered BIOM table (minimum sequence count: 22)"/>
+                    <has_text text="rarefied BIOM table (sampling depth: 22)"/>
+                    <has_text text="Beta diversity results"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test><!-- test suppressing all -->
+            <param name="input_biom_fp" value="core_diversity_analyses/otu_table.biom"/>
+            <param name="mapping_fp" value="core_diversity_analyses/map.txt"/>
+            <param name="sampling_depth" value="22"/>
+            <param name="parallel" value="--parallel"/>
+            <param name="nonphylogenetic_diversity" value="--nonphylogenetic_diversity"/>
+            <param name="suppress_taxa_summary" value="--suppress_taxa_summary"/>
+            <param name="suppress_beta_diversity" value="--suppress_beta_diversity"/>
+            <param name="suppress_alpha_diversity" value="--suppress_alpha_diversity"/>
+            <param name="suppress_group_significance" value="--suppress_group_significance"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Filtered BIOM table (minimum sequence count: 22)"/>
+                    <has_text text="rarefied BIOM table (sampling depth: 22)"/>
+                </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/core_diversity_analyses.html>`_.
+    ]]></help>
+    <citations>
+        <expand macro="citations"/>
+    </citations>
+</tool>