diff --git a/galaxy/wrapper/alignmentSieve.xml b/galaxy/wrapper/alignmentSieve.xml
index b6b5ef0d2b..b48c2d6319 100644
--- a/galaxy/wrapper/alignmentSieve.xml
+++ b/galaxy/wrapper/alignmentSieve.xml
@@ -7,8 +7,6 @@
     <expand macro="requirements"/>
     <command>
 <![CDATA[
-        #import re
-        #set label = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
         ln -s '$bamfile' one.bam &&
         #if $bamfile.ext == 'bam':
             ln -s '${bamfile.metadata.bam_index}' one.bam.bai &&
@@ -18,13 +16,10 @@
         @BINARY@
         @THREADS@
         -b one.bam
-        --label '$label'
         #if $filterRNAstrand:
             --filterRNAstrand '$filterRNAstrand'
         #end if
 
-        $ignoreDuplicates
-
         #if $minMappingQuality:
             --minMappingQuality $minMappingQuality
         #end if
@@ -45,14 +40,8 @@
             --maxFragmentLength $maxFragmentLength
         #end if
 
-        #if ' '.join( map(str, $blackListFileName) ) != 'None':
-            #set blfiles=[]
-            #for $f in $blackListFileName:
-                #silent $blfiles.append("'%s'" % $f)
-            #end for
-            #if $blfiles != ["'None'"]:
-                --blackListFileName #echo ' '.join($blfiles)#
-            #end if
+        #if $blackListFileName:
+            --blackListFileName '$blackListFileName'
         #end if
 
         #if $filterMetrics:
@@ -104,8 +93,6 @@
             <option value="forward">forward</option>
             <option value="reverse">reverse</option>
         </param>
-
-        <expand macro="ignoreDuplicates"/>
         <expand macro="minMappingQuality"/>
         <expand macro="samFlags"/>
         <expand macro="fragLength"/>
diff --git a/galaxy/wrapper/bamCompare.xml b/galaxy/wrapper/bamCompare.xml
index 6e654af427..f5f6b41672 100644
--- a/galaxy/wrapper/bamCompare.xml
+++ b/galaxy/wrapper/bamCompare.xml
@@ -45,7 +45,7 @@
                 #end if
             #end if
 
-            --operation $comparison.type
+            --operation '$comparison.type'
             $exactScaling
 
             #if $comparison.type in ['ratio','log2']:
@@ -157,10 +157,8 @@
             <when value="yes">
                 <expand macro="smoothLength"/>
                 <expand macro="read_processing_options"/>
-
                 <expand macro="skipNAs"/>
                 <expand macro="skipZeroOverZero"/>
-
                 <param argument="--ignoreForNormalization" type="text" value="" size="50"
                     label="regions that should be excluded for calculating the scaling factor"
                     help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor.
@@ -186,26 +184,35 @@
             <param name="showAdvancedOpt" value="no"/>
             <param name="outFileFormat" value="bedgraph"/>
             <param name="binSize" value="5"/>
-            <param name="type" value="ratio"/>
-            <output name="outFileName" file="bamCompare_result1.bg" ftype="bedgraph"/>
+            <conditional name="comparison">
+                <param name="type" value="ratio"/>
+            </conditional>
+            <output name="outFileName" ftype="bedgraph">
+                <assert_contents>
+                    <has_text_matching expression="chrM\t0\t16569\t1"/>
+                    <has_n_lines n="1"/>
+                </assert_contents>
+                has_n_lines
+            </output>
         </test>
         <test expect_num_outputs="1">
             <param name="bamFile1" value="bowtie2 test1.bam" ftype="bam"/>
             <param name="bamFile2" value="bowtie2 test1.bam" ftype="bam"/>
-            <param name="showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bigwig"/>
             <param name="binSize" value="10"/>
-            <param name="type" value="ratio"/>
+            <conditional name="comparison">
+                <param name="type" value="ratio"/>
+            </conditional>
             <output name="outFileName" file="bamCompare_result2.bw" ftype="bigwig"/>
         </test>
         <!-- Test with BAM and CRAM file as input-->
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testA.cram" ftype="cram"/>
-            <param name="showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="binSize" value="10"/>
-            <param name="type" value="ratio"/>
+            <conditional name="comparison">
+                <param name="type" value="ratio"/>
+            </conditional>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
                     <has_text_matching expression="3R\t0\t200\t1"/>
@@ -217,10 +224,15 @@
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testA.cram" ftype="cram"/>
-            <param name="showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="binSize" value="10"/>
-            <param name="type" value="substract"/>
+            <conditional name="scaling">
+                <param name="method" value="own"/>
+                <param name="scaleFactor1" value="1"/>
+                <param name="scaleFactor2" value="1"/>
+            </conditional>
+            <conditional name="comparison">
+                <param name="type" value="subtract"/>
+            </conditional>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
                     <has_text_matching expression="3R\t0\t200\t0"/>
@@ -232,10 +244,11 @@
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testB.bam" ftype="bam"/>
-            <param name="showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bedgraph"/>
             <param name="binSize" value="10"/>
-            <param name="type" value="ratio"/>
+            <conditional name="comparison">
+                <param name="type" value="subtract"/>
+            </conditional>
             <param name="pseudocount" value="1 1"/>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
@@ -250,11 +263,14 @@
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testB.bam" ftype="bam"/>
-            <param name="showAdvancedOpt" value="yes"/>
+            <conditional name="scaling">
+                <param name="method" value="own"/>
+                <param name="scaleFactor1" value="1"/>
+                <param name="scaleFactor2" value="1"/>
+            </conditional>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="binSize" value="10"/>
-            <param name="type" value="ratio"/>
-            <param name="skipZeroOverZero" value="--skipZeroOverZero"/>
+            <param name="showAdvancedOpt" value="yes"/>
+            <param name="skipZeroOverZero" value="true"/>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
                     <has_text_matching expression="3R\t50\t100\t0.571429"/>
@@ -267,10 +283,16 @@
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testB.bam" ftype="bam"/>
-            <param name="showAdvancedOpt" value="yes"/>
+            <conditional name="scaling">
+                <param name="method" value="own"/>
+                <param name="scaleFactor1" value="1"/>
+                <param name="scaleFactor2" value="1"/>
+            </conditional>
+            <conditional name="comparison">
+                <param name="type" value="subtract"/>
+            </conditional>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="binSize" value="10"/>
-            <param name="type" value="ratio"/>
+            <param name="showAdvancedOpt" value="yes"/>
             <param name="skipNAs" value="true"/>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml
index caa86a3100..a9edd002d9 100755
--- a/galaxy/wrapper/deepTools_macros.xml
+++ b/galaxy/wrapper/deepTools_macros.xml
@@ -5,8 +5,9 @@
     <token name="@GALAXY_VERSION@">23.2</token>
     <xml name="requirements">
         <requirements>
-            <!-- <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement> -->
-            <requirement type="package" version="1.21">samtools</requirement>
+            <container type="docker">quay.io/biocontainers/deeptools:4.0.0--h004ce86_0</container>
+            <!--requirement type="package" version="@TOOL_VERSION@">deeptools</requirement>
+            <requirement type="package" version="1.21">samtools</requirement-->
         </requirements>
         <expand macro="stdio"/>
         <version_command>@BINARY@ --version</version_command>
@@ -552,21 +553,16 @@ is vital to you, select Yes below.">
     </token>
 
     <xml name="blacklist">
-        <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
+        <!-- the current rust-based function supports only a single blacklist file. Hence removed the multiple="true" attribute -->
+        <param argument="--blackListFileName" type="data" format="bed,gtf" optional="true"
             label="Blacklisted regions in BED/GTF format"
             help="One or more files containing regions to exclude from the analysis"/>
     </xml>
 
     <token name="@blacklist@">
 <![CDATA[
-        #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
-            #set blfiles=[]
-            #for $f in $advancedOpt.blackListFileName:
-                #silent $blfiles.append("'%s'" % $f)
-            #end for
-            #if $blfiles != ["'None'"]:
-                --blackListFileName #echo ' '.join($blfiles)#
-            #end if
+        #if $advancedOpt.blackListFileName:
+            --blackListFileName '$advancedOpt.blackListFileName'
         #end if
 ]]>
     </token>
@@ -663,10 +659,9 @@ is vital to you, select Yes below.">
     </xml>
 
     <xml name="skipZeroOverZero">
-        <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
-            help="Skip bins where BOTH files lack coverage.">
-            <option value="" selected="true">No</option>
-            <option value="--skipZeroOverZero">Yes, skip them.</option>
+        <param argument="--skipZeroOverZero" type="boolean" truevalue="--skipZeroOverZero" falsevalue="" checked="False"
+        label="Skip bins of no coverage"
+        help="Skip bins where BOTH files lack coverage.">
         </param>
     </xml>
 
diff --git a/galaxy/wrapper/estimateReadFiltering.xml b/galaxy/wrapper/estimateReadFiltering.xml
index 925e8d0368..e0e7491fec 100644
--- a/galaxy/wrapper/estimateReadFiltering.xml
+++ b/galaxy/wrapper/estimateReadFiltering.xml
@@ -32,15 +32,8 @@
         #if $samFlagExclude:
             --samFlagExclude $samFlagExclude
         #end if
-
-        #if ' '.join( map(str, $blackListFileName) ) != 'None':
-            #set blfiles=[]
-            #for $f in $blackListFileName:
-                #silent $blfiles.append("'%s'" % $f)
-            #end for
-            #if $blfiles != ["'None'"]:
-                --blackListFileName #echo ' '.join($blfiles)#
-            #end if
+        #if $blackListFileName:
+            --blackListFileName '$blackListFileName'
         #end if
 ]]>
     </command>
@@ -55,7 +48,7 @@
             label="Distance between bins"
             help="To reduce the computation time, not every possible genomic bin is sampled. This option allows you to set the distance between bins actually sampled from. Larger numbers are sufficient for high coverage samples, while smaller values are useful for lower coverage samples. Note that if you specify a value that results in too few (&lt;1000) reads sampled, the value will be decreased." />
 
-        <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand." 
+        <param argument="filterRNAstrand" type="select" 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>
diff --git a/galaxy/wrapper/plotPCA.xml b/galaxy/wrapper/plotPCA.xml
index d81b43edbe..7344402f72 100644
--- a/galaxy/wrapper/plotPCA.xml
+++ b/galaxy/wrapper/plotPCA.xml
@@ -77,7 +77,7 @@
             <param name="plotTitle" value="Test Plot" />
             <param name="outFileFormat" value="png" />
             <param name="outFileNameData" value="True" />
-            <output name="outFileName" file="plotPCA_result2.png" ftype="png" compare="sim_size" delta="12000" />
+            <output name="outFileName" file="plotPCA_result1.png" ftype="png" compare="sim_size" delta="12000" />
             <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" lines_diff="2" />
         </test>
     </tests>
diff --git a/galaxy/wrapper/test-data/bamCompare_result1.bg b/galaxy/wrapper/test-data/bamCompare_result1.bg
deleted file mode 100644
index f4bea91a4f..0000000000
--- a/galaxy/wrapper/test-data/bamCompare_result1.bg
+++ /dev/null
@@ -1 +0,0 @@
-chrM	0	16569	1
diff --git a/galaxy/wrapper/test-data/bamCompare_result2.bw b/galaxy/wrapper/test-data/bamCompare_result2.bw
index d6d5c0438b..75b87e5000 100644
Binary files a/galaxy/wrapper/test-data/bamCompare_result2.bw and b/galaxy/wrapper/test-data/bamCompare_result2.bw differ
diff --git a/galaxy/wrapper/test-data/plotPCA_result2.png b/galaxy/wrapper/test-data/plotPCA_result2.png
deleted file mode 100644
index ad0ee26656..0000000000
Binary files a/galaxy/wrapper/test-data/plotPCA_result2.png and /dev/null differ