diff deseq2.xml @ 46:151ed7b41985 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 8f0f0f51f30cc630daebfeae8acae93e84dbd35c

--- a/deseq2.xml	Fri Dec 19 08:09:31 2025 +0000
+++ b/deseq2.xml	Tue Jan 06 11:22:10 2026 +0000
@@ -983,6 +983,44 @@
                 </assert_contents>
             </output>
         </test>
+        <!--Test sample_sheet_contrasts with numeric factor column in design formula -->
+        <test expect_num_outputs="2">
+            <param name="select_data|how" value="sample_sheet_contrasts"/>
+            <param name="select_data|countsFile">
+                <collection type="list">
+                    <element name="GSM461179_treat_single.counts" value="GSM461179_treat_single.counts"/>
+                    <element name="GSM461180_treat_paired.counts" value="GSM461180_treat_paired.counts"/>
+                    <element name="GSM461181_treat_paired.counts" value="GSM461181_treat_paired.counts"/>
+                    <element name="GSM461176_untreat_single.counts" value="GSM461176_untreat_single.counts"/>
+                    <element name="GSM461177_untreat_paired.counts" value="GSM461177_untreat_paired.counts"/>
+                    <element name="GSM461178_untreat_paired.counts" value="GSM461178_untreat_paired.counts"/>
+                    <element name="GSM461182_untreat_single.counts" value="GSM461182_untreat_single.counts"/>
+                </collection>
+            </param>
+            <param name="select_data|sample_sheet" value="sample_sheet_numeric.tab"/>
+            <param name="select_data|design_formula_mode|mode" value="custom"/>
+            <param name="select_data|design_formula_mode|design_formula" value="~ replicate + treatment"/>
+            <param name="select_data|design_formula_mode|reference_level" value="Untreated"/>
+            <section name="advanced_options">
+                <param name="use_beta_priors" value="1"/>
+            </section>
+            <section name="output_options">
+                <param name="output_selector" value="normCounts"/>
+            </section>
+            <output name="counts_out">
+                <assert_contents>
+                    <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
+                    <has_n_columns n="8"/>
+                </assert_contents>
+            </output>
+            <output name="deseq_out">
+                <assert_contents>
+                    <!-- Multi-factor design with numeric replicate column -->
+                    <has_text_matching expression="FBgn0003360\t1933\.950.*"/>
+                    <has_n_lines n="3999"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
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