diff --git a/test/functional/tools/for_workflows/mapper.xml b/test/functional/tools/for_workflows/mapper.xml
index 505e517c7db..3a6f325d475 100644
--- a/test/functional/tools/for_workflows/mapper.xml
+++ b/test/functional/tools/for_workflows/mapper.xml
@@ -1,7 +1,7 @@
 <tool id="mapper" name="Mapper" version="0.1.0">
-    <command>
-        cp $__tool_directory__/1.bam $out_file1
-    </command>
+    <command><![CDATA[
+cp '$__tool_directory__/1.bam' '$out_file1'
+    ]]></command>
     <inputs>
         <param name="input1" type="data" format="fastq" label="Fastq Input"/>
         <param name="reference" type="data" format="fasta" label="Fasta Input"/>
diff --git a/test/functional/tools/for_workflows/mapper2.xml b/test/functional/tools/for_workflows/mapper2.xml
index d3fb3b9d9a5..a800ef86616 100644
--- a/test/functional/tools/for_workflows/mapper2.xml
+++ b/test/functional/tools/for_workflows/mapper2.xml
@@ -1,29 +1,29 @@
 <tool id="mapper2" name="mapper2" version="0.1.0">
-    <command>
-        cp $__tool_directory__/1.bam $out_file1
-    </command>
+    <command><![CDATA[
+cp '$__tool_directory__/1.bam' '$out_file1'
+    ]]></command>
     <inputs>
         <!-- Conditional input block loosely based on bwa-mem. -->
         <conditional name="fastq_input">
-          <param name="fastq_input_selector" type="select" label="Single or Paired-end reads">
-            <option value="paired">Paired</option>
-            <option value="single">Single</option>
-            <option value="paired_collection">Paired Collection</option>
-            <option value="paired_iv">Paired Interleaved</option>
-          </param>
-          <when value="paired">
-            <param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" />
-            <param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" />
-          </when>
-          <when value="single">
-            <param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset"/>
-          </when>
-          <when value="paired_collection">
-            <param name="fastq_input1" format="fastq" type="data_collection" collection_type="paired" label="Select a paired collection" />
-          </when>
-          <when value="paired_iv">
-            <param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" />
-          </when>
+            <param name="fastq_input_selector" type="select" label="Single or Paired-end reads">
+                <option value="paired">Paired</option>
+                <option value="single">Single</option>
+                <option value="paired_collection">Paired Collection</option>
+                <option value="paired_iv">Paired Interleaved</option>
+            </param>
+            <when value="paired">
+                <param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" />
+                <param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" />
+            </when>
+            <when value="single">
+                <param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset"/>
+            </when>
+            <when value="paired_collection">
+                <param name="fastq_input1" type="data_collection" collection_type="paired" format="fastq" label="Select a paired collection" />
+            </when>
+            <when value="paired_iv">
+                <param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" />
+            </when>
         </conditional>
         <param name="reference" type="data" format="fasta" label="Fasta Input"/>
     </inputs>
diff --git a/test/functional/tools/for_workflows/pileup.xml b/test/functional/tools/for_workflows/pileup.xml
index df6c6af4149..aa17f109f03 100644
--- a/test/functional/tools/for_workflows/pileup.xml
+++ b/test/functional/tools/for_workflows/pileup.xml
@@ -1,9 +1,9 @@
 <tool id="pileup" name="Pileup" version="0.1.0">
-    <command>
-        printf "Summary" > $out_file1
-    </command>
+    <command><![CDATA[
+printf 'Summary' > '$out_file1'
+    ]]></command>
     <inputs>
-        <param name="input1" type="data" format="bam" multiple="true" label="BAM Inputs" min="1">
+        <param name="input1" type="data" format="bam" multiple="true" min="1" label="BAM Inputs">
             <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
         </param>
         <param name="reference" type="data" format="fasta" label="Fasta Input"/>
diff --git a/tools/filters/catWrapper.xml b/tools/filters/catWrapper.xml
index 33e67e1e5a4..d4865d3c5b9 100644
--- a/tools/filters/catWrapper.xml
+++ b/tools/filters/catWrapper.xml
@@ -1,13 +1,13 @@
 <tool id="cat1" name="Concatenate datasets" version="1.0.0">
     <description>tail-to-head</description>
-    <command interpreter="python">
-        catWrapper.py
-        $out_file1
-        $input1
-        #for $q in $queries
-            ${q.input2}
-        #end for
-    </command>
+    <command interpreter="python"><![CDATA[
+catWrapper.py
+'$out_file1'
+'$input1'
+#for $q in $queries
+    '${q.input2}'
+#end for
+    ]]></command>
     <inputs>
         <param name="input1" type="data" label="Concatenate Dataset"/>
         <repeat name="queries" title="Dataset">
@@ -33,8 +33,7 @@
         </test>
         -->
     </tests>
-    <help>
-
+    <help><![CDATA[
 .. class:: warningmark
 
 **WARNING:** Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This tool does not check if the datasets being concatenated are in the same format.
@@ -74,6 +73,5 @@ will result in the following::
     chr1  151278832  151279227  Z  0  -
     chr2  100000030  200000955  P  0  +
     chr2  100000015  200000999  Q  0  +
-
-    </help>
+    ]]></help>
 </tool>