--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaquantome_stat.xml	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,67 @@
+<tool id="metaquantome_stat" name="MetaQuantome Stats" version="@VERSION@.0">
+    <description>differential functional expression and taxonomic abundance</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @MAKE_SAMPS_TSV@
+        metaquantome stat
+        --samps samp_file.tab
+        --mode '$mode'
+        --ontology '$ontology'
+        --file '$file'
+        --parametric '$parametric'
+        $paired
+        --outfile='$outfile'
+    ]]></command>
+    <inputs>
+        <expand macro="SAMPS"/>
+        <param argument="--file" type="data" format="tabular" label="metaquantome expanded or filtered file"
+                    help=""/>
+        <param argument="--mode" type="select" label="Mode">
+            <option value="f">Functional analysis</option>
+            <option value="t">Taxonomic analysis</option>
+            <option value="ft">Functional-taxonomic interaction analysis</option>
+        </param>
+        <param name="ontology" type="select" label="Ontology">
+            <option value="go">Gene Ontology (column named 'go')</option>
+            <option value="ec">Gene Ontology (column named 'go')</option>
+            <option value="cog">COG (column named 'cog')</option>
+        </param>
+        <param argument="--parametric" type="select" label="Statistical test to perform">
+            <option value="False" selected="true">Wilcoxon test (nonparametric)</option>
+            <option value="True">standard t-test (parametric)</option>
+        </param>
+        <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" checked="false" label="Perform paired tests"/>
+        <expand macro="output_samples_choice"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" label="${tool.name} on ${on_string} stats"/>
+        <expand macro="output_samples"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="file" value="ec_ttest.tab" ftype="tabular" />
+            <param name="parametric" value="True" />
+            <param name="ontology" value="ec" />
+            <param name="mode" value="f" />
+            <output name="outfile" value="ec_ttest_tested.tab" ftype="tabular"/>
+            <!-- stat(expandfile, sinfo=TTEST_SINFO, paired=False, parametric=True, ontology='ec', mode='f',
+                      outfile=tested_file) -->
+            <param name="samps_src" value="build" />
+            <repeat name="samps">
+                <param name="group_name" value="s1"/>
+                <param name="col_names" value="int1,int2,int3"/>
+            </repeat>
+            <repeat name="samps">
+                <param name="group_name" value="s2"/>
+                <param name="col_names" value="int4,int5,int6"/>
+            </repeat>
+        </test>
+    </tests>
+    <help><![CDATA[
+        help
+    ]]></help>
+    <expand macro="citations" />
+</tool>