--- a/dada2_assignTaxonomyAddspecies.xml	Thu Dec 05 18:00:57 2019 -0500
+++ b/dada2_assignTaxonomyAddspecies.xml	Mon Mar 16 08:03:24 2020 -0400
@@ -29,6 +29,10 @@
 #end if
 tl <- strsplit(tl, ",")[[1]]
 
+#if str($seed)
+    set.seed($seed)
+#end if
+
 taxa <- assignTaxonomy(seqs, ref, minBoot = $minBoot, tryRC = $tryRC,
     outputBootstraps = $outputBootstraps,
     taxLevels = tl, multithread = nthreads, verbose=T)
@@ -53,7 +57,7 @@
 #end if
 write.table(taxa, file = '$output', quote = F, sep = "\t", row.names = T, col.names = NA)
 
-#if $outputBootstraps
+#if $outputBootstraps == "TRUE"
     write.table(boot, file = '$bootstraps', quote = F, sep = "\t", row.names = T, col.names = NA)
 #end if
     ]]></configfile>
@@ -122,6 +126,7 @@
                 <param argument="tryRC" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Try reverse complement" help="the reverse-complement of each sequence will be used for classification if it is a better match to the reference sequences than the forward sequence"/>
             </when>
         </conditional>
+        <param name="seed" type="integer" value="" optional="true" label="Seed" help="Seed for the random number renerator. Set it in order to reproduce exactly the same results."/>
     </inputs>
     <outputs>
         <data name="output" format="tabular" label="${tool.name} on ${on_string}"/>
@@ -132,41 +137,44 @@
     <tests>
         <!-- test w default params -->
         <test expect_num_outputs="1">
-            <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/>
+            <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo.tab"/>
             <param name="reference_cond|reference_select" value="history"/>
-            <param name="reference_cond|refFasta" ftype="fasta" value="reference.fa"/>
+            <param name="reference_cond|refFasta" ftype="fasta" value="reference.fa.gz"/>
             <param name="reference_cond|taxLevels" value="Level1,Level2,Level3,Level4,Level5" />
             <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
             <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="history"/>
-            <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta" value="reference_species.fa" />
-            <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" />
+            <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta" value="reference_species.fa.gz" />
+            <param name="seed" value="42"/>
+            <output name="output" value="assignTaxonomyAddspecies.tab" ftype="tabular" compare="sim_size" delta="0"/>
         </test>
          <!-- test w default params, bulit in reference -->
-        <test expect_num_outputs="1">
-            <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/>
+        <test expect_num_outputs="2">
+            <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo.tab"/>
             <param name="reference_cond|reference_select" value="builtin"/>
             <param name="reference_cond|refFasta" value="test_buildid"/>
+            <param name="outputBootstraps" value="TRUE" />
             <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
             <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="builtin"/>
             <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" value="test_buildid" />
-            <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" />
+            <param name="seed" value="42"/>
+            <output name="output" value="assignTaxonomyAddspecies.tab" ftype="tabular" compare="sim_size" delta="0" />
+            <output name="bootstraps" value="assignTaxonomyAddspecies_boot.tab" ftype="tabular" compare="sim_size" delta="100" />
         </test>
-        <!-- test w output bootstraps, minRC, note: sim_size for bootstraps output due to the probabilistics -->
-        <test expect_num_outputs="2">
-            <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/>
+        <!-- minRC, note: sim_size for bootstraps output due to the probabilistics -->
+        <test expect_num_outputs="1">
+            <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo.tab"/>
             <param name="reference_cond|reference_select" value="history"/>
-            <param name="reference_cond|refFasta" ftype="fasta" value="reference.fa"/>
+            <param name="reference_cond|refFasta" ftype="fasta.gz" value="reference.fa.gz"/>
             <param name="reference_cond|taxLevels" value="Level1,Level2,Level3,Level4,Level5" />
             <param name="minBoot" value="42" />
             <param name="tryRC" value="TRUE" />
-            <param name="outputBootstraps" value="TRUE" />
             <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
             <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="history"/>
-            <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta" value="reference_species.fa" />
+            <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta.gz" value="reference_species.fa.gz" />
             <param name="addSpecies_cond|allowMultiple" value="TRUE"/>
             <param name="addSpecies_cond|tryRC" value="TRUE" />
-            <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" compare="sim_size" />
-            <output name="bootstraps" value="assignTaxonomyAddspecies_F3D0_boot.tab" ftype="tabular" compare="sim_size" />
+            <param name="seed" value="42"/>
+            <output name="output" value="assignTaxonomyAddspecies.tab" ftype="tabular" compare="sim_size" />
         </test>
     </tests>
     <help><![CDATA[