--- a/goseq.xml	Fri Feb 26 13:31:00 2016 -0500
+++ b/goseq.xml	Sun Feb 28 11:52:10 2016 -0500
@@ -19,10 +19,13 @@
         --length_bias_plot "$length_bias_plot"
         --sample_vs_wallenius_plot "$sample_vs_wallenius_plot"
         --repcnt "$repcnt"
+        --use_genes_without_cat "$use_genes_without_cat"
     </command>
     <inputs>
         <param help="deseq2/edger/limma differential gene expression list" label="DGE list" name="dge_file" type="data" format="tabular" />
         <param help="Select the column that contains the multiple-testing corrected p-value" label="p adjust column" name="p_adj_column" type="data_column" numeric="true" data_ref="dge_file"/>
+        <param help="A boolean to indicate whether genes without a categorie should still be used. For example, a large number of gene may have no GO term annotated.  If this option is set to FALSE, those genes will be ignored in the calculation of p-values. If this option is set to TRUE, then these genes will count towards the total number of genes outside the category being tested"
+               name="use_genes_without_cat" label="Count genes without any category" type="boolean"/>
         <param help="Typically 0.05 after multiple testing correction" max="1" label="Minimum p adjust value to consider genes as differentially expressed" name="p_adj_cutoff" type="float" value="0.05" />
         <conditional name="source">
             <param help="This is needed if the gene length is not available in goseq. e.g. hg38 and mm10." label="Use gene length file?" name="use_length_file" type="select">