Mercurial > repos > iuc > limma_voom

changeset 23:e827f9aae031 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
author iuc
date Mon, 29 Nov 2021 11:05:15 +0000
parents 708348a17fa1
children 32511f586472
files limma_voom.xml
diffstat 1 files changed, 9 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- 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">