--- a/rmarkdown_deseq2_count_matrix.xml	Sat Dec 30 00:25:38 2017 -0500
+++ b/rmarkdown_deseq2_count_matrix.xml	Sat Dec 30 16:39:39 2017 -0500
@@ -17,11 +17,12 @@
 Rscript '${__tool_directory__}/rmarkdown_deseq2_count_matrix_render.R'
                         -e $echo
                         -c $count_data
+                        -n '$count_matrix_column_names'
                         -C $col_data
                         -D '$design_formula'
                         -k $contrast_condition
                         -T $treatment
-                        -k $control
+                        -K $control
                         -r $report
                         -d $report.files_path
                         -s $sink_message
@@ -31,21 +32,32 @@
         <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False"
                truevalue="TRUE" falsevalue="FALSE"/>
         <param type="data" name="count_data" label="count data" optional="False" format="txt,csv" multiple="False"/>
-        <param type="data" name="col_data" label="column data" optional="False" format="txt,csv" multiple="False"/>
+        <param type="text" name="count_matrix_column_names" label="column names"
+               help="This field is used to update the column names of count data matrix. Column names are separated by comma (,). For example, 'column_1, column_2, column_3, column_4'"
+               optional="True" area="True" size="5x25"></param>
+        <param type="data" name="col_data" label="column data (from file)" optional="False" format="txt,csv" multiple="False"/>
         <param type="text" name="design_formula" label="design formula"
                help="The simplest design formula for differential expression would be ~ condition, where condition&#13;&#10;                     is a column in colData(dds) that specifies which of two (or more groups) the samples belong to"
-               optional="False" value="~ condition_1 + condition_2"/>
+               optional="False" value="~ condition_1 + condition_2">
+            <sanitizer>
+                <valid>
+                    <add value="~"/>
+                </valid>
+            </sanitizer>
+        </param>
         <param type="text" name="contrast_condition" label="condition"
                help="A condition name specified in the design formula" optional="False" value="condition_1"/>
         <param type="text" name="treatment" label="treatment" help="the name of the numerator level for the fold change"
-               optional="False"/>
+               optional="False" value="treated"/>
         <param type="text" name="control" label="control" help="the name of the denominator level for the fold change"
-               optional="False"/>
+               optional="False" value="untreated"/>
     </inputs>
     <outputs>
         <data name="report" format="html" label="DESeq2 report" hidden="false"/>
         <data name="differential_genes" format="csv" label="differential genes" from_work_dir="differential_genes.csv"
               hidden="false"/>
+        <data name="deseq2" format="rdata" label="DESeq2 R objects" from_work_dir="deseq2.RData"
+              hidden="false"/>
         <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"
               hidden="false"/>
     </outputs>