--- a/cuffnorm_wrapper.xml	Sun Feb 19 12:08:50 2017 -0500
+++ b/cuffnorm_wrapper.xml	Tue Jun 16 16:58:39 2020 +0000
@@ -4,8 +4,8 @@
       <import>cuff_macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <version_command>cuffnorm 2>&amp;1 | head -n 1</version_command>
-    <command detect_errors="aggressive">
+    <version_command><![CDATA[cuffnorm 2>&1 | head -n 1]]></version_command>
+    <command detect_errors="aggressive"><![CDATA[
         cuffnorm
             --no-update-check
             --num-threads="\${GALAXY_SLOTS:-4}"
@@ -22,10 +22,10 @@
                 $advanced_settings.hits_norm
             #end if
             ## Inputs.
-            $gtf_input
+            '$gtf_input'
 
             @CONDITION_SAMPLES@
-    </command>
+    ]]></command>
     <inputs>
         <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/>
         <expand macro="condition_inputs" />
@@ -165,12 +165,28 @@
         </data>
     </outputs>
     <tests>
-        <!-- 
-        <test>
-                NOTE: as of version 0.0.6 of the wrapper, tests cannot be run because multiple inputs to a repeat
-                element are not supported.
+        <test expect_num_outputs="8">
+            <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf"/>
+            <conditional name="in_type">
+                <param name="set_in_type" value="BAM"/>
+                <repeat name="conditions">
+                    <param name="name" value="in1"/>
+                    <param name="samples" value="cuffdiff_in1.sam" ftype="sam"/>
+                </repeat>
+                <repeat name="conditions">
+                    <param name="name" value="in2"/>
+                    <param name="samples" value="cuffdiff_in2.sam" ftype="sam"/>
+                </repeat>
+            </conditional>
+            <output ftype="tabular" name="cds_fpkm_table" value="cds.fpkm_table"/>
+            <output ftype="tabular" name="cds_count_table" value="cds.count_table"/>
+            <output ftype="tabular" name="tss_groups_fpkm_table" value="tss_groups.fpkm_table"/>
+            <output ftype="tabular" name="tss_groups_count_table" value="tss_groups.count_table"/>
+            <output ftype="tabular" name="genes_fpkm_table" value="genes.fpkm_table"/>
+            <output ftype="tabular" name="genes_count_table" value="genes.count_table"/>
+            <output ftype="tabular" name="isoforms_fpkm_table" value="isoforms.fpkm_table"/>
+            <output ftype="tabular" name="isoforms_count_table" value="isoforms.count_table"/>
         </test>
-        -->
     </tests>
 
     <help>
@@ -222,7 +238,5 @@
   --compatible-hits-norm         With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes.
   --total-hits-norm              With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator
     </help>
-    <citations>
-        <citation type="doi">10.1038/nbt.1621</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>