--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jackknifed_beta_diversity.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,121 @@
+<tool id="qiime_jackknifed_beta_diversity" name="Perform jackknifed UPGMA 
+    clustering" version="1.9.1">
+
+    <description>and building jackknifed PCoA plots</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <version_command><![CDATA[
+        jackknifed_beta_diversity.py --version
+    ]]>
+    </version_command>
+
+    <stdio>
+        <regex match="VisibleDeprecationWarning"
+               source="both"
+               level="warning"
+               description="VisibleDeprecationWarning on numpy for `rank`" />
+        <regex match="RuntimeWarning: The result contains negative eigenvalues"
+               source="both"
+               level="warning"
+               description="Presence of negative eigenvalues" />
+        <regex match="Error"
+               source="both"
+               level="error"
+               description="Error" />
+    </stdio>
+
+    <command>
+<![CDATA[  
+        jackknifed_beta_diversity.py 
+            -i $otu_table_fp
+            -m $mapping_fp
+            -o jackknifed_beta_diversity
+            -e $seqs_per_sample
+
+            #if $tree_fp
+                -t $tree_fp
+            #end if
+
+            #if $parameter_fp
+                -p $parameter_fp
+            #end if
+
+            --master_tree $master_tree
+
+            $parallel
+            -O "\${GALAXY_SLOTS:-4}"
+        &&
+
+        python $__tool_directory__/jackknifed_beta_diversity_through_plots_html_generation.py 
+            --data_directory jackknifed_beta_diversity
+            --html_file $jackknifed_beta_diversity_report
+            --html_dir $jackknifed_beta_diversity_report.files_path     
+
+    ]]>
+    </command>
+
+    <inputs>
+        <param name="otu_table_fp" type="data" format="tabular,txt,tsv,biom" 
+            label="OTU table" help="(-i/--otu_table_fp)" 
+            multiple="True"/>
+
+        <param name="mapping_fp" type="data" format="tabular,txt,tsv" 
+            label="Mapping file" help="(-m/--mapping_fp)" 
+            multiple="True"/>
+
+        <param name="seqs_per_sample" type="integer" value="" label="Number of 
+            sequences to include in each jackknifed subset" 
+            help="(-e/--seqs_per_sample)"/>
+
+        <param name="tree_fp" type="data" format="txt" 
+            label="Tree file (Optional)" help="It is required for phylogenetic
+            measures (-t/--tree_fp)" 
+            optional="True"/>
+
+        <param name="parameter_fp" type="data" format="txt" 
+            label="Parameter file (Optional)" help="It specifies changes to the 
+            default behavior, e.g. beta diversity metrics (-p/--parameter_fp)" 
+            optional="true"/>
+
+        <param name="master_tree" type="select" 
+            label="Method for computing master trees in jackknife analysis" 
+            help="(--master_tree)">
+            <option value="consensus" selected="True">Consensus of trees from jackknifed otu tables</option>
+            <option value="full">Tree generated from input (unsubsambled) otu table</option>
+        </param>
+
+        <param name="parallel" type="boolean" label="Run in parallel where 
+            available?" truevalue="--parallel" falsevalue="" checked="true" 
+            help="(-a, --parallel)" />
+
+    </inputs>
+
+    <outputs>
+        <data format="html" name="jackknifed_beta_diversity_report" 
+            label="${tool.name} on ${on_string}: Report"/>
+    </outputs>
+
+    <tests>
+        <test>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+This tool performs jackknifing (repeatedly resampling a subset of the available data from each sample) to measure robustness of individual UPGMA clusters and clusters in PCoA plots.
+
+More information about this tool is available on 
+`QIIME documentation <http://qiime.org/scripts/jackknifed_beta_diversity.html>`_.
+    ]]>
+    </help>
+
+    <citations>
+        <expand macro="citations" />
+    </citations>
+</tool>