diff --git a/galaxy/wrapper/alignmentSieve.xml b/galaxy/wrapper/alignmentSieve.xml
index 425f0908..24829025 100644
--- a/galaxy/wrapper/alignmentSieve.xml
+++ b/galaxy/wrapper/alignmentSieve.xml
@@ -19,14 +19,14 @@
         @THREADS@
         -b one.bam
         --label '$label'
-        #if str($filterRNAstrand) != 'no':
+        #if $filterRNAstrand:
             --filterRNAstrand '$filterRNAstrand'
         #end if
 
         $ignoreDuplicates
 
         #if $minMappingQuality:
-            --minMappingQuality '$minMappingQuality'
+            --minMappingQuality $minMappingQuality
         #end if
 
         #if $samFlagInclude:
@@ -98,10 +98,9 @@
                   take strand into consideration for strand-specific
                   protocols. Note that only properly paired reads are considered."/>
         <param argument="--ATACshift" type="boolean" label="Shift fragment ends as appropriate for ATAC-seq"/>
-        <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand."
+        <param argument="filterRNAstrand" type="select" optional="true" label="Only include reads originating from fragments from the forward or reverse strand."
             help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
                   Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
-            <option value="no" selected="true">no</option>
             <option value="forward">forward</option>
             <option value="reverse">reverse</option>
         </param>
diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml
index 6dae6702..e6c3d83a 100755
--- a/galaxy/wrapper/deepTools_macros.xml
+++ b/galaxy/wrapper/deepTools_macros.xml
@@ -49,7 +49,7 @@
         $advancedOpt.ignoreDuplicates
         $advancedOpt.centerReads
         #if $advancedOpt.minMappingQuality:
-            --minMappingQuality '$advancedOpt.minMappingQuality'
+            --minMappingQuality $advancedOpt.minMappingQuality
         #end if
         #if $advancedOpt.samFlagInclude:
             --samFlagInclude $advancedOpt.samFlagInclude
@@ -716,7 +716,7 @@ is vital to you, select Yes below.">
     </xml>
 
     <xml name="output_dpi">
-        <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
+        <param argument="--dpi" type="integer" value="200" size="3" optional="True"
             label="Image dpi" help=""/>
     </xml>
 
diff --git a/galaxy/wrapper/multiBamSummary.xml b/galaxy/wrapper/multiBamSummary.xml
index dc1a504c..c198a260 100644
--- a/galaxy/wrapper/multiBamSummary.xml
+++ b/galaxy/wrapper/multiBamSummary.xml
@@ -97,13 +97,13 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <param name="modeOpt" value="bins" />
             <param name="binSize" value="10" />
             <output name="outFile" file="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <param name="modeOpt" value="BED-file" />
             <param name="region_file" value="multiBamSummary_regions.bed" />
diff --git a/galaxy/wrapper/multiBigwigSummary.xml b/galaxy/wrapper/multiBigwigSummary.xml
index cbcdde3a..b63db25d 100644
--- a/galaxy/wrapper/multiBigwigSummary.xml
+++ b/galaxy/wrapper/multiBigwigSummary.xml
@@ -19,7 +19,7 @@
             --outFileName $outFile
 
             --bwfiles #echo ' '.join($files)#
-            
+
             #if $custom_sample_labels_conditional.custom_labels_select == 'Yes'
                 --labels #echo ' '.join($custom_sample_labels_conditional.labels)#
             #end if
@@ -86,13 +86,13 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
             <param name="modeOpt" value="bins" />
             <param name="binSize" value="10" />
             <output name="outFile" file="multiBigwigSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
             <param name="modeOpt" value="bins" />
             <param name="binSize" value="10" />
diff --git a/galaxy/wrapper/plotCorrelation.xml b/galaxy/wrapper/plotCorrelation.xml
index d8c60640..3313acb1 100644
--- a/galaxy/wrapper/plotCorrelation.xml
+++ b/galaxy/wrapper/plotCorrelation.xml
@@ -109,14 +109,14 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
             <param name="outFileFormat" value="png" />
             <param name="outFileCorMatrix" value="True" />
             <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" />
             <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="400" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
             <param name="outFileFormat" value="png" />
             <param name="whatToPlot" value="scatterplot" />
diff --git a/galaxy/wrapper/plotCoverage.xml b/galaxy/wrapper/plotCoverage.xml
index 6b50af26..ab514ce1 100644
--- a/galaxy/wrapper/plotCoverage.xml
+++ b/galaxy/wrapper/plotCoverage.xml
@@ -114,7 +114,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <!--param name="outFileFormat" value="png" /-->
             <param name="showAdvancedOpt" value="yes" />
@@ -123,7 +123,7 @@
             <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
             <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="plotTitle" value="Test Title from Galaxy" />
diff --git a/galaxy/wrapper/plotEnrichment.xml b/galaxy/wrapper/plotEnrichment.xml
index 1e34adc9..955f737a 100644
--- a/galaxy/wrapper/plotEnrichment.xml
+++ b/galaxy/wrapper/plotEnrichment.xml
@@ -48,7 +48,7 @@
                 $advancedOpt.perSample
 
                 $advancedOpt.variableScales
-                
+
                 $advancedOpt.perSample
 
                 $advancedOpt.variableScales
@@ -175,7 +175,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <param name="BED" value="multiBamSummary_regions.bed,multiBamSummary_regions.bed" ftype="bed" />
             <param name="outRawCounts" value="true" />
diff --git a/galaxy/wrapper/plotFingerprint.xml b/galaxy/wrapper/plotFingerprint.xml
index dea1ccb9..436e0c2a 100644
--- a/galaxy/wrapper/plotFingerprint.xml
+++ b/galaxy/wrapper/plotFingerprint.xml
@@ -114,13 +114,13 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <param name="showAdvancedOpt" value="no" />
             <param name="showOutputSettings" value="no" />
             <output name="outFileName" file="plotFingerprint_result1.png" ftype="png" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="showOutputSettings" value="yes" />
diff --git a/galaxy/wrapper/plotHeatmap.xml b/galaxy/wrapper/plotHeatmap.xml
index 79141cfc..c81f3a5e 100644
--- a/galaxy/wrapper/plotHeatmap.xml
+++ b/galaxy/wrapper/plotHeatmap.xml
@@ -143,12 +143,13 @@
                 <param argument="--sortUsingSamples" type="text"
                     label="List of samples to be used for sorting"
                     help="List of sample numbers (order as in matrix), which are used by --sortUsing for sorting.
-                    If no value is set, it uses all samples. Example: 1 3 (space separated!)" />
+                    If no value is set, it uses all samples. Example: 1 3 (space separated!)">
                     <sanitizer>
                         <valid initial="string.printable">
                             <add value=" "/>
                         </valid>
                     </sanitizer>
+                </param>
                 <param argument="--linesAtTickMarks" type="boolean" truevalue="--linesAtTickMarks" falsevalue=""
                     label="Draw dashed lines in heatmap above all tick marks?" />
                 <param argument="--averageTypeSummaryPlot" type="select"
@@ -246,12 +247,13 @@
                 <param argument="--clusterUsingSamples" type="text"
                     label="List of samples to be used for clustering"
                     help="List of sample numbers (order as in matrix), which are used by --kmeans or --hclust for clustering.
-                    If no value is set, it uses all samples. Example: 1 3 (space separated!)"/>
+                    If no value is set, it uses all samples. Example: 1 3 (space separated!)">
                     <sanitizer>
                         <valid initial="string.printable">
                             <add value=" "/>
                         </valid>
                     </sanitizer>
+                </param>
             </when>
         </conditional>
     </inputs>
@@ -261,11 +263,11 @@
         <expand macro="output_save_matrix_values" />
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
             <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="4000" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="whatToShow" value="heatmap and colorbar" />
diff --git a/galaxy/wrapper/plotPCA.xml b/galaxy/wrapper/plotPCA.xml
index 27b781f8..d81b43ed 100644
--- a/galaxy/wrapper/plotPCA.xml
+++ b/galaxy/wrapper/plotPCA.xml
@@ -44,16 +44,16 @@
             <when value="no" />
             <when value="yes">
                 <expand macro="plotWidthHeight" PLOTWIDTH="10.0" PLOTHEIGHT="10.0" />
-                <param name="PCs" argument="--PCs" label="Principal components to plot" value="1 2" type="text"
+                <param argument="--PCs" label="Principal components to plot" value="1 2" type="text"
                     help="The principal components to plot. If specified, you must provide two different integers, greater than zero, separated by a space. An example (and the default) is '1 2'." />
-                <param name="ntop" argument="--ntop" label="Number of rows to use" value="1000" type="integer"
+                <param argument="--ntop" label="Number of rows to use" value="1000" type="integer"
                     help="Use only the top N most variable rows in the original matrix. Specifying 0 will result in all rows being used. If the matrix is to be transposed, rows with 0 variance are always excluded, even if a values of 0 is specified. The default is 1000." />
-                <param name="log2" argument="--log2" type="boolean" truevalue="--log2" falsevalue="" label="log2 transform data" help="log2 transform the datapoints prior to computing the PCA. Note that 0.01 is added to all values to prevent 0 values from becoming -infinity. Using this option with input that contains negative values will result in an error." />
+                <param argument="--log2" type="boolean" truevalue="--log2" falsevalue="" label="log2 transform data" help="log2 transform the datapoints prior to computing the PCA. Note that 0.01 is added to all values to prevent 0 values from becoming -infinity. Using this option with input that contains negative values will result in an error." />
                 <param argument="--transpose" type="boolean" label="Transpose Matrix?" help="Perform the PCA on the transpose of the matrix, (i.e., with samples as rows and features/genes as columns). This then matches what is typically done in R for RNAseq data." truevalue="--transpose" falsevalue="" />
                 <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically. This option is not applicable if the PCA is performed on the transposed matrix." truevalue="--rowCenter" falsevalue="" />
-                <param argument="--colors" type="text" name="colors" label="Symbol colors" value="" optional="True"
+                <param argument="--colors" type="text" label="Symbol colors" value="" optional="True"
                     help="A list of colors for the symbols. Color names and html hex string (e.g., #eeff22) are accepted. The color names should be space separated. For example, --colors 'red blue green'. If not specified, the symbols will be given automatic colors." />
-                <param argument="--markers" type="text" name="markers" label="Custom markers" value="" optional="True"
+                <param argument="--markers" type="text" label="Custom markers" value="" optional="True"
                     help="A list of markers for the symbols. (e.g., '&lt;','&gt;','o') are accepted. The marker values should be space separated. For example, 's' 'o' 's' 'o'. If not specified, the symbols will be given automatic shapes." />
             </when>
         </conditional>
@@ -65,14 +65,14 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="corData" value="multiBamSummary_result2b.npz" ftype="deeptools_coverage_matrix" />
             <param name="plotTitle" value="Test Plot" />
             <param name="outFileFormat" value="png" />
             <param name="showAdvancedOpt" value="yes" />
             <output name="outFileName" file="plotPCA_result1.png" ftype="png" compare="sim_size" delta="12000" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="corData" value="multiBamSummary_result2b.npz" ftype="deeptools_coverage_matrix" />
             <param name="plotTitle" value="Test Plot" />
             <param name="outFileFormat" value="png" />
diff --git a/galaxy/wrapper/plotProfiler.xml b/galaxy/wrapper/plotProfiler.xml
index cdccb815..ff7d7d07 100644
--- a/galaxy/wrapper/plotProfiler.xml
+++ b/galaxy/wrapper/plotProfiler.xml
@@ -194,11 +194,11 @@
 
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
             <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="4000" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="showScaleRegionsOpt" value="yes" />
diff --git a/galaxy/wrapper/test-data/heatmapper_result1.png b/galaxy/wrapper/test-data/heatmapper_result1.png
index fa368635..02ad533b 100644
Binary files a/galaxy/wrapper/test-data/heatmapper_result1.png and b/galaxy/wrapper/test-data/heatmapper_result1.png differ
diff --git a/galaxy/wrapper/test-data/multiBamSummary_result1.npz b/galaxy/wrapper/test-data/multiBamSummary_result1.npz
index 1a591f1d..17942962 100644
Binary files a/galaxy/wrapper/test-data/multiBamSummary_result1.npz and b/galaxy/wrapper/test-data/multiBamSummary_result1.npz differ
diff --git a/galaxy/wrapper/test-data/multiBamSummary_result2.npz b/galaxy/wrapper/test-data/multiBamSummary_result2.npz
index d0df013d..0fe68993 100644
Binary files a/galaxy/wrapper/test-data/multiBamSummary_result2.npz and b/galaxy/wrapper/test-data/multiBamSummary_result2.npz differ
diff --git a/galaxy/wrapper/test-data/multiBigwigSummary_result1.npz b/galaxy/wrapper/test-data/multiBigwigSummary_result1.npz
index 9614fa1d..fb3e2c85 100644
Binary files a/galaxy/wrapper/test-data/multiBigwigSummary_result1.npz and b/galaxy/wrapper/test-data/multiBigwigSummary_result1.npz differ
diff --git a/galaxy/wrapper/test-data/multiBigwigSummary_result2.npz b/galaxy/wrapper/test-data/multiBigwigSummary_result2.npz
index 471e3e00..2fb767bc 100644
Binary files a/galaxy/wrapper/test-data/multiBigwigSummary_result2.npz and b/galaxy/wrapper/test-data/multiBigwigSummary_result2.npz differ
diff --git a/galaxy/wrapper/test-data/plotCorrelation_result1.png b/galaxy/wrapper/test-data/plotCorrelation_result1.png
index 726ff8bf..a0f7558e 100644
Binary files a/galaxy/wrapper/test-data/plotCorrelation_result1.png and b/galaxy/wrapper/test-data/plotCorrelation_result1.png differ
diff --git a/galaxy/wrapper/test-data/plotCorrelation_result2.png b/galaxy/wrapper/test-data/plotCorrelation_result2.png
index c144cf38..db092d9b 100644
Binary files a/galaxy/wrapper/test-data/plotCorrelation_result2.png and b/galaxy/wrapper/test-data/plotCorrelation_result2.png differ
diff --git a/galaxy/wrapper/test-data/plotCoverage_result1.png b/galaxy/wrapper/test-data/plotCoverage_result1.png
index ae7874e0..e22727ca 100644
Binary files a/galaxy/wrapper/test-data/plotCoverage_result1.png and b/galaxy/wrapper/test-data/plotCoverage_result1.png differ
diff --git a/galaxy/wrapper/test-data/plotEnrichment_output.png b/galaxy/wrapper/test-data/plotEnrichment_output.png
index 9b50e0db..6302d954 100644
Binary files a/galaxy/wrapper/test-data/plotEnrichment_output.png and b/galaxy/wrapper/test-data/plotEnrichment_output.png differ
diff --git a/galaxy/wrapper/test-data/plotFingerprint_result1.png b/galaxy/wrapper/test-data/plotFingerprint_result1.png
index b32939ec..4608c1c7 100644
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diff --git a/galaxy/wrapper/test-data/plotFingerprint_result2.png b/galaxy/wrapper/test-data/plotFingerprint_result2.png
index 313d014e..3efef836 100644
Binary files a/galaxy/wrapper/test-data/plotFingerprint_result2.png and b/galaxy/wrapper/test-data/plotFingerprint_result2.png differ
diff --git a/galaxy/wrapper/test-data/plotPCA_result1.png b/galaxy/wrapper/test-data/plotPCA_result1.png
index 4ce59d72..ad0ee266 100644
Binary files a/galaxy/wrapper/test-data/plotPCA_result1.png and b/galaxy/wrapper/test-data/plotPCA_result1.png differ
diff --git a/galaxy/wrapper/test-data/plotPCA_result2.png b/galaxy/wrapper/test-data/plotPCA_result2.png
index 4ce59d72..ad0ee266 100644
Binary files a/galaxy/wrapper/test-data/plotPCA_result2.png and b/galaxy/wrapper/test-data/plotPCA_result2.png differ
diff --git a/galaxy/wrapper/test-data/plotPCA_result2.tabular b/galaxy/wrapper/test-data/plotPCA_result2.tabular
index f2b79eed..ebdc6ff7 100644
--- a/galaxy/wrapper/test-data/plotPCA_result2.tabular
+++ b/galaxy/wrapper/test-data/plotPCA_result2.tabular
@@ -1,4 +1,4 @@
 #plotPCA --outFileNameData
 Component	bowtie2-test1.bam	bowtie2-test1.bam	Eigenvalue
 1	-0.7071067811865476	-0.7071067811865475	4.0
-2	-0.7071067811865475	0.7071067811865476	2.49319462166397e-32
+2	-0.7071067811865475	0.7071067811865476	1.2325951644078315e-32
diff --git a/galaxy/wrapper/test-data/profiler_result1.png b/galaxy/wrapper/test-data/profiler_result1.png
index a0f14d8b..6bdfb4ad 100644
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diff --git a/galaxy/wrapper/test-data/profiler_result2.png b/galaxy/wrapper/test-data/profiler_result2.png
index d9f166c8..2e67acf1 100644
Binary files a/galaxy/wrapper/test-data/profiler_result2.png and b/galaxy/wrapper/test-data/profiler_result2.png differ