# HG changeset patch
# User iuc
# Date 1638183915 0
# Node ID e827f9aae03185be69104987b4dfa14d3164d6c6
# Parent  708348a17fa1f8aa21a3866075d4e581bfdc3cb8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"

diff -r 708348a17fa1 -r e827f9aae031 limma_voom.xml
--- a/limma_voom.xml	Sat Jun 26 19:10:16 2021 +0000
+++ b/limma_voom.xml	Mon Nov 29 11:05:15 2021 +0000
@@ -1,7 +1,10 @@
-<tool id="limma_voom" name="limma" version="3.48.0+galaxy1">
+<tool id="limma_voom" name="limma" version="@TOOL_VERSION@+galaxy2">
     <description>
         Perform differential expression with limma-voom or limma-trend
     </description>
+    <macros>
+        <token name="@TOOL_VERSION@">3.48.0</token>
+    </macros>
     <xrefs>
         <xref type="bio.tools">limma</xref>
     </xrefs>
@@ -14,7 +17,7 @@
     </edam_operations>
 
     <requirements>
-        <requirement type="package" version="3.48.0">bioconductor-limma</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-limma</requirement>
         <requirement type="package" version="3.34.0">bioconductor-edger</requirement>
         <requirement type="package" version="1.4.36">r-statmod</requirement>
         <requirement type="package" version="1.1.1">r-scales</requirement>
@@ -271,8 +274,8 @@
                         </param>
                         <when value="cpm">
                             <param name="cpmReq" type="float" value="1" min="0" label="Minimum CPM" help="Treat genes with CPM below this value as unexpressed and filter out. See the Filter Low Counts section below for more information."/>
-                             <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
-                             help="Filter out all genes that do not meet the Minimum CPM in at least this many samples. See the Filter Low Counts section below for more information."/>
+                            <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
+                                help="Filter out all genes that do not meet the Minimum CPM in at least this many samples. See the Filter Low Counts section below for more information."/>
                         </when>
                         <when value="counts">
                             <param name="cntReq" type="integer" value="0" min="0" label="Minimum Count" help="Filter out all genes that do not meet this minimum count. You can choose below to apply this filter to the total count for all samples or specify the number of samples under Minimum Samples. See the Filter Low Counts section below for more information." />
@@ -281,9 +284,7 @@
                                     <option value="total">Total</option>
                                     <option value="sample">Sample</option>
                                 </param>
-                                <when value="total">
-                                    <param name="totReq" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Filter on Total Count" help="Apply the Minimum Count filter to genes after summing counts for all samples. See the Filter Low Counts section below for more information." />
-                                </when>
+                                <when value="total"/>
                                 <when value="sample">
                                     <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
                                     help="Filter out all genes that do not meet the Minimum Count in at least this many samples. See the Filter Low Counts section below for more information."/>
@@ -728,7 +729,7 @@
                 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
             </repeat>
             <param name="cfile" value="yes" />
-            <param name="cinfo" value="contrasts.txt" />
+            <param name="cinfo" value="contrasts.txt" ftype="tabular" />
             <param name="normalisationOption" value="TMM" />
             <param name="topgenes" value="6" />
             <output_collection name="outTables" count="3">