diff limma_voom.xml @ 26:119b069fc845 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738

--- a/limma_voom.xml	Tue Mar 01 08:03:53 2022 +0000
+++ b/limma_voom.xml	Fri Feb 09 17:06:25 2024 +0000
@@ -1,13 +1,12 @@
-<tool id="limma_voom" name="limma" version="@TOOL_VERSION@+galaxy0">
+<tool id="limma_voom" name="limma" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>
         Perform differential expression with limma-voom or limma-trend
     </description>
     <macros>
-        <token name="@TOOL_VERSION@">3.50.1</token>
+        <token name="@TOOL_VERSION@">3.58.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">23.0</token>
     </macros>
-    <xrefs>
-        <xref type="bio.tools">limma</xref>
-    </xrefs>
     <edam_topics>
         <edam_topic>topic_3308</edam_topic>
     </edam_topics>
@@ -15,16 +14,20 @@
         <edam_operation>operation_3563</edam_operation>
         <edam_operation>operation_3223</edam_operation>
     </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">limma</xref>
+        <xref type="bioconductor">limma</xref>
+    </xrefs>
 
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bioconductor-limma</requirement>
-        <requirement type="package" version="3.36.0">bioconductor-edger</requirement>
-        <requirement type="package" version="1.4.36">r-statmod</requirement>
-        <requirement type="package" version="1.1.1">r-scales</requirement>
+        <requirement type="package" version="4.0.2">bioconductor-edger</requirement>
+        <requirement type="package" version="1.5.0">r-statmod</requirement>
+        <requirement type="package" version="1.3.0">r-scales</requirement>
         <requirement type="package" version="0.2.21">r-rjson</requirement>
-        <requirement type="package" version="1.20.3">r-getopt</requirement>
-        <requirement type="package" version="3.1.1">r-gplots</requirement>
-        <requirement type="package" version="2.4.0">bioconductor-glimma</requirement>
+        <requirement type="package" version="1.20.4">r-getopt</requirement>
+        <requirement type="package" version="3.1.3.1">r-gplots</requirement>
+        <requirement type="package" version="2.12.0">bioconductor-glimma</requirement>
     </requirements>
 
     <version_command><![CDATA[
@@ -733,6 +736,12 @@
             <param name="normalisationOption" value="TMM" />
             <param name="topgenes" value="6" />
             <output_collection name="outTables" count="3">
+                <element name="limma-voom_Mut-WT-WT-Mut" ftype="tabular" >
+                     <assert_contents>
+                        <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
+                        <has_text_matching expression="11304.*0.9146" />
+                    </assert_contents>
+                </element>
                 <element name="limma-voom_Mut-WT" ftype="tabular" >
                     <assert_contents>
                         <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
@@ -745,12 +754,6 @@
                         <has_text_matching expression="11304.*-0.4573" />
                     </assert_contents>
                 </element>
-                <element name="limma-voom_Mut-WT-WT-Mut" ftype="tabular" >
-                     <assert_contents>
-                        <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
-                        <has_text_matching expression="11304.*0.9146" />
-                    </assert_contents>
-                </element>
             </output_collection>
         </test>
     </tests>