--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compare_biom.xml	Sat Jan 20 03:31:34 2018 -0500
@@ -0,0 +1,130 @@
+<tool id="picrust_compare_biom" name="Compare BIOM tables" version="@WRAPPER_VERSION@.0">
+    <description>Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+        compare_biom.py
+            -e '$expected'
+            -o '$outfile'
+            $not_relative_abundance_scores
+            $advanced.normalize
+            $advanced.limit_to_observed_observations
+            $advanced.limit_to_expected_observations
+            $advanced.shuffle_samples
+
+            '$observed'
+    ]]></command>
+    <inputs>
+        <param name="observed" type="data" format="biom1" label="Observed table" help="The observed table of either relative abundance or real counts"/>
+        <param name="expected" type="data" format="biom1" label="Expected table" help="The expected table of either relative abundance or real counts"/>
+        <param argument="not_relative_abundance_scores" type="boolean" truevalue="--not_relative_abundance_scores" falsevalue="" checked="false" label="Real counts instead of relative abundances?"
+               help="Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN"/>
+        <section name="advanced" title="Advanced parameters" expanded="false">
+            <param argument="compare_observations" type="boolean" truevalue="--compare_observations" falsevalue="" checked="false" label="Compare observations"
+                help="Calculate accuracy values by comparing between observations (instead of between samples)."/>
+            <param argument="normalize" type="boolean" truevalue="--normalize" falsevalue="" checked="false" label="Normalize?"
+                help="Convert both expected and observed tables to relative abundances (instead of observations)."/>
+            <param argument="limit_to_observed_observations" type="boolean" truevalue="--limit_to_observed_observations" falsevalue="" checked="false" label="Limit to observed observations?"
+                help="Ignore observations that are not in the observed table."/>
+            <param argument="limit_to_expected_observations" type="boolean" truevalue="--limit_to_expected_observations" falsevalue="" checked="false" label="Limit to expected observations?"
+                help="Ignore observations that are not in the expected table."/>
+            <param argument="shuffle_samples" type="boolean" truevalue="--shuffle_samples" falsevalue="" checked="false" label="Shuffle samples?"
+                help="Shuffle samples ids randomly before measuring accuracy."/>
+        </section>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" label="${tool.name} on ${on_string} Comparison summary"/>
+    </outputs>
+    <tests>
+        <test><!-- relative abundance test -->
+            <param name="observed" value="observed_ra.biom" ftype="biom1"/>
+            <param name="expected" value="expected_ra.biom" ftype="biom1"/>
+            <output name="outfile" ftype="tabular">
+                <assert_contents>
+                    <has_text_matching expression="file\tlabel\taccuracy"/>
+                    <has_text text="sample1"/>
+                    <has_text text="sample3"/>
+                    <has_text text="sample2"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test><!-- real counts test -->
+            <param name="observed" value="observed.biom" ftype="biom1"/>
+            <param name="expected" value="expected.biom" ftype="biom1"/>
+            <param name="not_relative_abundance_scores" value="--not_relative_abundance_scores"/>
+            <output name="outfile" ftype="tabular">
+                <assert_contents>
+                    <has_text_matching expression="file\tlabel\taccuracy"/>
+                    <has_text text="sample1"/>
+                    <has_text text="sample3"/>
+                    <has_text text="sample2"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test><!-- all other switches test -->
+            <param name="observed" value="observed.biom" ftype="biom1"/>
+            <param name="expected" value="expected.biom" ftype="biom1"/>
+            <param name="not_relative_abundance_scores" value="--not_relative_abundance_scores"/>
+            <param name="compare_observations" value="--compare_observations"/>
+            <param name="normalize" value="--normalize"/>
+            <param name="limit_to_observed_observations" value="--limit_to_observed_observations"/>
+            <param name="shuffle_samples" value="--shuffle_samples"/>
+            <output name="outfile" ftype="tabular">
+                <assert_contents>
+                    <has_text_matching expression="file\tlabel\taccuracy"/>
+                    <has_text text="sample1"/>
+                    <has_text text="sample3"/>
+                    <has_text text="sample2"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+@PICRUST_OVERVIEW@
+
+**Command Documentation**
+
+Compare an observed table to an expected table using either relative abundance or real counts.
+
+**Input files:**
+
+**Observed table:** A table of observed relative abundances or real counts in .biom format.
+
+**Expected table:** The expected table of relative abundances or real counts in .biom format.
+
+**Output file:** Tab delimited file with various accuracy metrics.
+
+**Optional Parameters:**
+
+*compare observations*
+
+    Calculate accuracy values by comparing between observations (instead of between samples) [default: False]
+
+*normalize*
+
+    Convert both expected and observed tables to relative abundances (instead of observations) [default: False]
+
+*limit to expected observations*
+
+    Ignore observations that are not in the expected table[default: False]
+
+*limit to observed observations*
+
+    Ignore observations that are not in the observed table[default: False]
+
+*shuffle samples*
+
+    Shuffle samples ids randomly before measuring accuracy[default: False]
+
+*not relative abundance scores*
+
+    Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN [default: False]
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>