--- a/macros.xml	Mon Jan 06 15:18:20 2020 -0500
+++ b/macros.xml	Wed Jan 08 13:01:03 2020 -0500
@@ -313,20 +313,44 @@
         </data>
     </xml>
 
+    
+    <xml name="test_defaults_log">
+        <test>
+            <param name="genomes" ftype="fasta" value="Enterococcus_casseliflavus_EC20.fasta,Enterococcus_faecalis_T2.fna,Enterococcus_faecalis_TX0104.fa"/>
+            <output name="log">
+                <assert_contents>
+                    <yield/>
+                </assert_contents>
+            </output>
+        </test>
+    </xml>
+
     <token name="@GENOMES_HELP@"><![CDATA[
 I/O PARAMETERS:
   -g [GENOMES [GENOMES ...]], --genomes [GENOMES [GENOMES ...]]
-                        genomes to cluster in .fasta format (default: None)
+                        genomes to cluster in .fasta format
+                        (default: None)
+
+
 ]]></token>
 
     <token name="@FILTERING_HELP@"><![CDATA[
 FILTERING OPTIONS:
   -l LENGTH, --length LENGTH
-                        Minimum genome length (default: 50000)
+                        Minimum genome length
+                        (default: 50000)
+
+
   -comp COMPLETENESS, --completeness COMPLETENESS
-                        Minumum genome completeness (default: 75)
+                        Minumum genome completeness
+                        (default: 75)
+
+
   -con CONTAMINATION, --contamination CONTAMINATION
-                        Maximum genome contamination (default: 25)
+                        Maximum genome contamination
+                        (default: 25)
+
+
   --ignoreGenomeQuality
                         Don't run checkM or do any quality filtering. NOT
                         RECOMMENDED! This is useful for use with
@@ -341,12 +365,14 @@
 GENOME COMPARISON PARAMETERS:
   -ms MASH_SKETCH, --MASH_sketch MASH_SKETCH
                         MASH sketch size (default: 1000)
+
   --S_algorithm {goANI,ANIn,ANImf,gANI}
                         Algorithm for secondary clustering comaprisons:
                         ANImf = (RECOMMENDED) Align whole genomes with nucmer; filter alignment; compare aligned regions
                         ANIn  = Align whole genomes with nucmer; compare aligned regions
                         gANI  = Identify and align ORFs; compare aligned ORFS
-                         (default: ANImf)
+                        (default: ANImf)
+
   -n_PRESET {normal,tight}
                         Presets to pass to nucmer
                         tight   = only align highly conserved regions
@@ -360,12 +386,14 @@
                         ANI threshold to form primary (MASH) clusters
                         (default: 0.9)
   -sa S_ANI, --S_ani S_ANI
-                        ANI threshold to form secondary clusters (default:
-                        0.99)
+                        ANI threshold to form secondary clusters
+                        (default: 0.99)
+
   --SkipMash            Skip MASH clustering, just do secondary clustering on
                         all genomes (default: False)
-  --SkipSecondary       Skip secondary clustering, just perform MASH
-                        clustering (default: False)
+  --SkipSecondary       Skip secondary clustering, just perform MASH clustering
+                        (default: False)
+
   -nc COV_THRESH, --cov_thresh COV_THRESH
                         Minmum level of overlap between genomes when doing
                         secondary comparisons (default: 0.1)
@@ -374,7 +402,8 @@
                         (for ANIn/ANImf only; gANI can only do larger method)
                         total   = 2*(aligned length) / (sum of total genome lengths)
                         larger  = max((aligned length / genome 1), (aligned_length / genome2))
-                         (default: larger)
+                        (default: larger)
+
   --clusterAlg CLUSTERALG
                         Algorithm used to cluster genomes (passed to
                         scipy.cluster.hierarchy.linkage (default: average)
@@ -398,17 +427,26 @@
   -sizeW SIZE_WEIGHT, --size_weight SIZE_WEIGHT
                         weight of log(genome size) (default: 0)
 
+
 ]]></token>
 
     <token name="@TAXONOMY_HELP@"><![CDATA[
 TAXONOMY:
-  --run_tax             generate taxonomy information (Tdb) (default: False)
+  --run_tax             generate taxonomy information (Tdb)
+                        (default: False)
+
   --tax_method {percent,max}
                         Method of determining taxonomy
                         percent = The most descriptive taxonimic level with at least (per) hits
-                        max     = The centrifuge taxonomic level with the most overall hits (default: percent)
+                        max     = The centrifuge taxonomic level with the most overall hits
+                        (default: percent)
+
+
   -per PERCENT, --percent PERCENT
-                        minimum percent for percent method (default: 50)
+                        minimum percent for percent method
+                        (default: 50)
+
+
   --cent_index CENT_INDEX
                         path to centrifuge index (for example,
                         /home/mattolm/download/centrifuge/indices/b+h+v