--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann_rna_dna_norm.xml	Wed May 12 09:01:24 2021 +0000
@@ -0,0 +1,117 @@
+<tool id="humann_rna_dna_norm" name="Normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description> combined meta'omic sequencing data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+humann_rna_dna_norm
+    --input_dna '$input_dna'
+    --input_rna '$input_rna'
+    --output_basename 'results'
+    --method '$method'
+#if $log.log_transform == 'yes'
+    --log_transform
+    --log_base $log.log_base
+#end if
+    ]]></command>
+    <inputs>
+        <param argument="--input_dna" type="data" format="tsv,tabular,biom1" label="Original DNA output table"/>
+        <param argument="--input_rna" type="data" format="tsv,tabular,biom1" label="Original RNA output table"/>
+        <param argument="--method" type="select" label="Choice of smoothing method">
+            <option value="laplace">Laplace</option>
+            <option value="witten_bell">Witten-Bell</option>
+        </param>
+        <conditional name="log">
+            <param argument="--log_transform" type="select" label="Report log-transformed relative expression values?">
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param argument="--log_base" type="integer" value="2" label="Base for log transformation"/>
+            </when>
+            <when value="no"/>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="relative_expression" from_work_dir="results-relative_expression.tsv" label="${tool.name} on ${on_string}: Normalized RNA"/>
+        <data format="tabular" name="smoothed_dna" from_work_dir="results-smoothed_dna.tsv" label="${tool.name} on ${on_string}: Smoothed DNA"/>
+        <data format="tabular" name="smoothed_rna" from_work_dir="results-smoothed_rna.tsv" label="${tool.name} on ${on_string}: Smoothed RNA"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="3">
+            <param name="input_dna" value="rna_dna_norm-dna.txt"/>
+            <param name="input_rna" value="rna_dna_norm-rna.txt"/>
+            <param name="method" value="laplace"/>
+            <conditional name="log">
+                <param name="log_transform" value="no"/>
+            </conditional>
+            <output name="relative_expression" ftype="tabular">
+                <assert_contents>
+                    <has_text text="A|1"/>
+                    <has_text text="0.285714"/>
+                    <has_n_columns n="3"/>
+                </assert_contents>
+            </output>
+            <output name="smoothed_dna" ftype="tabular">
+                <assert_contents>
+                    <has_text text="A|1"/>
+                    <has_text text="13"/>
+                    <has_n_columns n="3"/>
+                </assert_contents>
+            </output>
+            <output name="smoothed_rna" ftype="tabular">
+                <assert_contents>
+                    <has_text text="A|1"/>
+                    <has_text text="62"/>
+                    <has_n_columns n="3"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="3">
+            <param name="input_dna" value="rna_dna_norm-dna.txt"/>
+            <param name="input_rna" value="rna_dna_norm-rna.txt"/>
+            <param name="method" value="witten_bell"/>
+            <conditional name="log">
+                <param name="log_transform" value="yes"/>
+                <param name="log_base" value="2"/>
+            </conditional>
+            <output name="relative_expression" ftype="tabular">
+                <assert_contents>
+                    <has_text text="A|1"/>
+                    <has_text text="0.118644"/>
+                    <has_n_columns n="3"/>
+                </assert_contents>
+            </output>
+            <output name="smoothed_dna" ftype="tabular">
+                <assert_contents>
+                    <has_text text="A|1"/>
+                    <has_text text="9.24"/>
+                    <has_n_columns n="3"/>
+                </assert_contents>
+            </output>
+            <output name="smoothed_rna" ftype="tabular">
+                <assert_contents>
+                    <has_text text="A|1"/>
+                    <has_text text="39.4545"/>
+                    <has_n_columns n="3"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+Given a DNA table and a RNA table, this tool produces smoothed RNA and DNA values as well as relative expression values. 
+
+"Smoothing" means substituting a small value in place of a zero or missing value. 
+The default method used is "Laplace" (pseudocount) scaling, where the pseudocount is the sample-specific minimum non-zero value (Witten-Bell smoothing is also implemented.)
+
+The DNA and RNA columns must be 1:1 and in the same order.
+
+If working with stratified data, smoothing is carried out on the stratified values and then community totals are recomputed.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>