--- a/deseq2.xml	Mon Nov 29 18:16:48 2021 +0000
+++ b/deseq2.xml	Fri Aug 26 11:16:15 2022 +0000
@@ -92,6 +92,10 @@
     #if $batch_factors:
         --batch_factors '$batch_factors'
     #end if
+    #if $advanced_options.prefilter_conditional.prefilter:
+        $advanced_options.prefilter_conditional.prefilter
+        -V $advanced_options.prefilter_conditional.prefilter_value
+    #end if
     #if $advanced_options.outlier_replace_off:
         -a
     #end if
@@ -194,6 +198,19 @@
             <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
                 label="Turn off independent filtering"
                 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
+            <conditional name="prefilter_conditional">
+                <param name="prefilter" type="select" label="Perform pre-filtering" help="While it is not necessary to pre-filter 
+                    low count genes before running the DESeq2 functions, there are two reasons which make pre-filtering useful: 
+                    by removing rows in which there are very few reads, we reduce the required memory, and we increase the speed. 
+                    It can also improve visualizations, as features with no information for differential expression are not plotted.">
+                    <option value="-P">Enabled</option>
+                    <option value="" selected="true">Disabled</option>
+                </param>
+                <when value="-P">
+                    <param name="prefilter_value" type="integer" min="0" value="10" label="Pre-filter value" help="Keep only rows that have at least N reads total." />
+                </when>
+                <when value=""/>
+            </conditional>
         </section>
         <section name="output_options" title="Output options">
             <param name="output_selector" type="select" multiple="True" optional="true" display="checkboxes" label="Output selector">
@@ -272,6 +289,7 @@
             <output name="deseq_out" >
                 <assert_contents>
                     <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" />
+                    <has_n_lines n="3999"/>
                 </assert_contents>
             </output>
         </test>
@@ -579,6 +597,39 @@
                 </assert_contents>
             </output>
         </test>
+        <!--Test prefilter parameter -->
+        <test expect_num_outputs="2">
+            <repeat name="rep_factorName">
+                <param name="factorName" value="Treatment"/>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" value="Treated"/>
+                    <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" value="Untreated"/>
+                    <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
+                </repeat>
+            </repeat>
+            <section name="advanced_options">
+                <conditional name="prefilter_conditional">
+                    <param name="prefilter" value="-P"/>
+                    <param name="prefilter_value" value="10"/>
+                </conditional>
+            </section>
+            <section name="output_options">
+                <param name="output_selector" value="normCounts"/>
+            </section>
+            <output name="counts_out">
+                <assert_contents>
+                    <has_n_lines n="2922"/>
+                </assert_contents>
+            </output>
+            <output name="deseq_out" >
+                <assert_contents>
+                    <has_n_lines n="2921"/>  <!-- Smallen value when compared with the first test-->
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark