--- a/cuffdiff_wrapper.xml	Sun Feb 19 12:11:27 2017 -0500
+++ b/cuffdiff_wrapper.xml	Tue Jun 16 16:57:20 2020 +0000
@@ -1,12 +1,12 @@
 <tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.5">
     <description>find significant changes in transcript expression, splicing, and promoter use</description>
     <macros>
-      <import>cuff_macros.xml</import>
+        <import>cuff_macros.xml</import>
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="2.16.0">bioconductor-cummerbund</requirement>
     </expand>
-    <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
+    <version_command><![CDATA[cuffdiff 2>&1 | head -n 1]]></version_command>
     <command detect_errors="aggressive"><![CDATA[
         cuffdiff
             --no-update-check
@@ -175,8 +175,8 @@
                     help="Instructs Cuffdiff to analyze the provided samples as a time series, rather than testing for differences between all pairs of samples. Samples should be provided in increasing time order at the command line (e.g first time point SAM, second timepoint SAM, etc.)" />
                 <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" />
                 <param name="hits_norm" type="select" label="Hits included in normalization" help="All Hits: 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. Compatible Hits: 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. It is active by default." >
-                        <option value="--compatible-hits-norm" selected="True">Compatible Hits</option>
-                        <option value="--total-hits-norm">All Hits</option>
+                    <option value="--compatible-hits-norm" selected="True">Compatible Hits</option>
+                    <option value="--total-hits-norm">All Hits</option>
                 </param>
                 <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus"
                     help="Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 500,000" />
@@ -398,7 +398,5 @@
   --num-frag-assign-draws        For each fragment drawn from a transcript, Cuffdiff will assign it this many times (probabilistically), thus estimating the assignment uncertainty for each transcript. Used to estimate the variance-covariance matrix on assigned fragment counts.
   --min-reps-for-js-test         Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates.
     </help>
-    <citations>
-        <citation type="doi">10.1038/nbt.1621</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>