# HG changeset patch
# User iuc
# Date 1637355798 0
# Node ID ed9e8345a292672a7e6044b9ec421a022a5ed602
# Parent  b30a443484ab112b2d3d655cc514e6702028c3aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit a3c52d23c261ef0bd0cc4c3d59900e108ca3f67e"

diff -r b30a443484ab -r ed9e8345a292 deseq2.xml
--- a/deseq2.xml	Mon Jun 28 05:13:50 2021 +0000
+++ b/deseq2.xml	Fri Nov 19 21:03:18 2021 +0000
@@ -193,9 +193,9 @@
                 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
         </section>
         <section name="output_options" title="Output options">
-            <param name="output_selector" type="select" multiple="True" display="checkboxes" label="Output selector">
+            <param name="output_selector" type="select" multiple="True" optional="true" display="checkboxes" label="Output selector">
                 <option value="pdf" selected="True">Generate plots for visualizing the analysis results</option>
-                <option value="normCounts">Output rLog normalized table</option>
+                <option value="normCounts">Output normalised counts</option>
                 <option value="normVST">Output VST normalized table</option>
                 <option value="normRLog">Output rLog normalized table</option>
                 <option value="many_contrasts">Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)</option>
diff -r b30a443484ab -r ed9e8345a292 deseq2_macros.xml
--- a/deseq2_macros.xml	Mon Jun 28 05:13:50 2021 +0000
+++ b/deseq2_macros.xml	Fri Nov 19 21:03:18 2021 +0000
@@ -20,20 +20,20 @@
     </xml>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.22.1">bioconductor-deseq2</requirement>
+            <requirement type="package" version="1.34.0">bioconductor-deseq2</requirement>
             <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->
-            <requirement type="package" version="2.26.2">bioconductor-rhdf5</requirement>
-            <requirement type="package" version="1.10.0">bioconductor-tximport</requirement>
-            <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>
-            <requirement type="package" version="1.20.2">r-getopt</requirement>
-            <requirement type="package" version="0.8.0">r-ggrepel</requirement>
-            <requirement type="package" version="3.0.1">r-gplots</requirement>
-            <requirement type="package" version="1.0.10">r-pheatmap</requirement>
+            <requirement type="package" version="2.38.0">bioconductor-rhdf5</requirement>
+            <requirement type="package" version="1.22.0">bioconductor-tximport</requirement>
+            <requirement type="package" version="1.46.1">bioconductor-genomicfeatures</requirement>
+            <requirement type="package" version="1.20.3">r-getopt</requirement>
+            <requirement type="package" version="0.9.1">r-ggrepel</requirement>
+            <requirement type="package" version="3.1.1">r-gplots</requirement>
+            <requirement type="package" version="1.0.12">r-pheatmap</requirement>
             <requirement type="package" version="0.2.20">r-rjson</requirement>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">2.11.40.6</token>
-    <token name="@SUFFIX_VERSION@">2</token>
+    <token name="@TOOL_VERSION@">2.11.40.7</token>
+    <token name="@SUFFIX_VERSION@">0</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_3308</edam_topic>