--- a/sleuth.xml	Thu Jun 08 19:57:53 2023 +0000
+++ b/sleuth.xml	Mon Jun 02 21:31:22 2025 +0000
@@ -1,5 +1,5 @@
 <tool id="sleuth" name="Sleuth" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE@">
-    <description>differential expression analysis</description>
+    <description>Differential expression analysis</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -9,15 +9,15 @@
         <regex match="Execution halted"
            source="both"
            level="fatal"
-           description="Execution halted." />
+           description="Execution halted."/>
         <regex match="Error in"
            source="both"
            level="fatal"
-           description="An undefined error occurred, please check your input carefully and contact your administrator." />
+           description="An undefined error occurred, please check your input carefully and contact your administrator."/>
         <regex match="Fatal error"
            source="both"
            level="fatal"
-           description="An undefined error occurred, please check your input carefully and contact your administrator." />
+           description="An undefined error occurred, please check your input carefully and contact your administrator."/>
     </stdio>
     <version_command><![CDATA[echo $(R --version | grep version | grep -v GNU)", sleuth version" $(R --vanilla --slave -e "library(sleuth); cat(sessionInfo()\$otherPkgs\$sleuth\$Version)" 2> /dev/null | grep -v -i "WARNING: ")]]></version_command>
     <command><![CDATA[
@@ -74,7 +74,7 @@
                     <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
                         help="Only letters, numbers and underscores will be retained in this field">
                         <sanitizer>
-                            <valid initial="string.letters,string.digits"><add value="_" /></valid>
+                            <valid initial="string.letters,string.digits"><add value="_"/></valid>
                         </sanitizer>
                     </param>
                     <param name="countsFile" type="data" format="h5" multiple="true" label="Counts file(s)"/>
@@ -82,26 +82,26 @@
             </when>
             <when value="complex">
                 <param name="countsFile" type="data_collection" format="h5" multiple="true" label="Counts file(s)"/>
-                <param argument="--metadata_file" type="data" format="txt" label="Input metadata file" help="You can find more details about the format of the design table in the help section." />
+                <param argument="--metadata_file" type="data" format="txt" label="Input metadata file" help="You can find more details about the format of the design table in the help section."/>
             </when>
         </conditional>
         <section name="advanced_options" title="Advanced options" expanded="true">
             <param argument="normalization" type="boolean" truevalue="--normalize" falsevalue="" checked="true" label="Normalize data" 
                 help="If this is set to false, bootstraps will not be read and transformation of the data will not be done. This should 
-                    only be set to false if one desires to do a quick check of the raw data. " />
+                    only be set to false if one desires to do a quick check of the raw data. "/>
             <param argument="nbins" type="integer" min="0" value="100" label="NBins" help="The number of bins that the data should be 
-                split for the sliding window shrinkage using the mean-variance curve." />
+                split for the sliding window shrinkage using the mean-variance curve."/>
             <param argument="lwr" type="float" min="0" max="1" value="0.25" label="LWR" help="The lower range of variances within each 
-                bin that should be included for the shrinkage procedure. " />
+                bin that should be included for the shrinkage procedure. "/>
             <param argument="upr" type="float" min="0" max="1" value="0.75" label="UPR" help="The upper range of variances within each 
-                bin that should be included for the shrinkage procedure." />
+                bin that should be included for the shrinkage procedure."/>
         </section>
 
     </inputs>
     <outputs>
         <data name="sleuth_table" from_work_dir="sleuth_table.tab" format="tabular" label="${tool.name} on ${on_string}: DE table">
             <actions>
-                <action name="column_names" type="metadata" default="target_id,pval,qval,test_stat,rss,degrees_free,mean_obs,var_obs,tech_var,sigma_sq,smooth_sigma_sq,final_sigma_sq" />
+                <action name="column_names" type="metadata" default="target_id,pval,qval,test_stat,rss,degrees_free,mean_obs,var_obs,tech_var,sigma_sq,smooth_sigma_sq,final_sigma_sq"/>
             </actions>
         </data>
         <data name="pca_plot" from_work_dir="pca_plot.pdf" format="pdf" label="${tool.name} on ${on_string}: PCA plot"/>
@@ -154,7 +154,7 @@
             </section>
             <output name="sleuth_table" ftype="tabular">
                 <assert_contents>
-                    <has_size value="756310" delta="100"/>
+                    <has_size value="756425" delta="100"/>
                     <has_text text="ENST00000394894.8"/>
                     <has_text text="ENST00000524187.1"/>
                 </assert_contents>
@@ -183,7 +183,7 @@
             </section>
             <output name="sleuth_table" ftype="tabular">
                 <assert_contents>
-                    <has_size value="756310" delta="100"/>
+                    <has_size value="756425" delta="100"/>
                     <has_text text="ENST00000394894.8"/>
                     <has_text text="ENST00000524187.1"/>
                 </assert_contents>
@@ -230,5 +230,5 @@
 Additional factors can be included in the design table.
 
     ]]></help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>