--- a/kraken_biom.xml	Sat Sep 03 22:13:08 2022 +0000
+++ b/kraken_biom.xml	Fri Sep 09 09:32:59 2022 +0000
@@ -11,6 +11,9 @@
        ln -s '$s' './$i-kraken_report.tabular' &&
     #end if
 #end for
+#if $metadata
+    ln -s '$metadata' './metadata.tsv' &&
+#end if
 kraken-biom
 #for $i, $s in enumerate($kraken_reports)
     #if $s
@@ -23,8 +26,11 @@
 #if $min
     --min $min
 #end if
+#if $metadata
+    --metadata 'metadata.tsv'
+#end if
 #if $otu_fp
-    --otu_fp '$otu_fp'
+    --otu_fp 'OTU_FP'
 #end if
 #if $fmt
     --fmt $fmt
@@ -40,6 +46,7 @@
             <option value="F">F</option>
             <option value="G">G</option>
             <option value="S">S</option>
+            <option value="SS">SS</option>
         </param>
         <param argument="--min" type="select" optional="true" label="Min" help="Reads assigned at and below min rank will be recorded as being assigned to the min rank level. Default: S">
             <option value="O">O</option>
@@ -49,8 +56,10 @@
             <option value="F">F</option>
             <option value="G">G</option>
             <option value="S" selected="true">S</option>
+            <option value="SS">SS</option>
         </param>
-        <param argument="--otu_fp" type="data" optional="true" format="tabular" label="OTU FP" help="Create a file containing just the (NCBI) OTU IDs for use with a service such as phyloT (http://phylot.biobyte.de/) to generate a phylogenetic tree for use in downstream analysis such as UniFrac, iTol (itol.embl.de), or PhyloToAST (phylotoast.org)"/>
+        <param argument="--metadata" type="data" format="tabular" optional="true" label="Sample metadata file" help="This should be in TSV or CSV (Tabular) format. The first column should be the Sample ID (e.g. 0-kraken_report, 1-kraken_report, etc.). This is the same name as the input files. If no metadata is given, basic metadata is added to support importing the BIOM table into sites like phinch (http://phinch.org/index.html). Example for metadata files: http://qiime.org/documentation/ file_formats.html#mapping-file-overview"/>
+        <param name="otu_fp" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Do you want to create an OTU IDs file" help="Create a file containing just the (NCBI) OTU IDs for use with a service such as phyloT (http://phylot.biobyte.de/) to generate a phylogenetic tree for use in downstream analysis such as UniFrac, iTol (itol.embl.de), or PhyloToAST (phylotoast.org)"/>
         <param argument="--fmt" type="select" optional="true" label="Output Format" help="Set the output format of the BIOM table. Default is HDF5">
             <option value="tsv">TSV</option>
             <option value="json">JSON</option>
@@ -58,18 +67,21 @@
         </param>
     </inputs>
     <outputs>
-        <data name="biomOutput" format="biom2" from_work_dir="./table.biom" label="Kraken biom output file">
+        <data name="biomOutput" format="tabular" from_work_dir="./table.biom" label="Kraken-biom output file">
             <change_format>
-                <when input="fmt" value="json" format="json" />
+                <when input="fmt" value="json" format="biom1" />
+            </change_format> 
+            <change_format>
+                <when input="fmt" value="hdf5" format="biom2" />
             </change_format>
-            <change_format>
-                <when input="fmt" value="tsv" format="tsv" />
-            </change_format>    
-        </data>       
+        </data>
+        <data name="otuOutput" format="mothur.map" from_work_dir="./OTU_FP" label="OTU File">       
+            <filter>otu_fp is True</filter>
+        </data>     
     </outputs>  
     <tests>
     <test expect_num_outputs="1">
-        <param name="kraken_reports" value="krakenReport1.tabular,krakenReport2.tabular,krakenReport3.tabular"/>
+        <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/>
         <param name="fmt" value="hdf5"/>
         <output name="biomOutput" ftype="biom2">
             <assert_contents>
@@ -78,9 +90,9 @@
         </output>
     </test>
     <test expect_num_outputs="1">
-        <param name="kraken_reports" value="krakenReport1.tabular,krakenReport2.tabular,krakenReport3.tabular"/>
+        <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/>
         <param name="fmt" value="tsv"/>
-        <output name="biomOutput" ftype="tsv">
+        <output name="biomOutput" ftype="tabular">
             <assert_contents>
                 <has_n_lines n="8246"/>
                 <has_text text="Constructed from biom file"/>
@@ -88,14 +100,45 @@
         </output>
     </test>    
     <test expect_num_outputs="1">
-        <param name="kraken_reports" value="krakenReport1.tabular,krakenReport2.tabular,krakenReport3.tabular"/>
+        <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/>
         <param name="fmt" value="json"/>
-        <output name="biomOutput" ftype="json">
+        <output name="biomOutput" ftype="biom1">
+            <assert_contents>
+                <has_text text="Biological Observation"/>
+            </assert_contents>
+        </output>
+    </test>
+    <test expect_num_outputs="2">
+        <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/>
+        <param name="otu_fp" value="true"/>
+        <param name="fmt" value="json"/>
+        <output name="biomOutput" ftype="biom1">
             <assert_contents>
                 <has_text text="Biological Observation"/>
             </assert_contents>
         </output>
-    </test>        
+        <output name="otuOutput" ftype="mothur.map">
+            <assert_contents>
+                <has_n_lines n="8244"/>
+            </assert_contents>
+        </output>
+    </test>
+    <test expect_num_outputs="2">
+        <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/>
+        <param name="metadata" value="SamplesMetaDataTabular.csv"/>        
+        <param name="otu_fp" value="true"/>
+        <param name="fmt" value="json"/>
+        <output name="biomOutput" ftype="biom1">
+            <assert_contents>
+                <has_text text="Biological Observation"/>
+            </assert_contents>
+        </output>
+        <output name="otuOutput" ftype="mothur.map">
+            <assert_contents>
+                <has_n_lines n="8244"/>
+            </assert_contents>
+        </output>
+    </test>    
     </tests>
     <help><![CDATA[
 Kraken-biom