diff limma_voom.xml @ 7:e6a4ff41af6b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33

--- a/limma_voom.xml	Tue May 08 18:12:40 2018 -0400
+++ b/limma_voom.xml	Wed May 09 13:27:14 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="limma_voom" name="limma" version="3.34.9.2">
+<tool id="limma_voom" name="limma" version="3.34.9.3">
     <description>
         Perform differential expression with limma-voom or limma-trend
     </description>
@@ -10,10 +10,11 @@
         <requirement type="package" version="0.5.0">r-scales</requirement>
         <requirement type="package" version="0.2.15">r-rjson</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="3.0.1">r-gplots</requirement>
     </requirements>
 
     <version_command><![CDATA[
-echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
     ]]></version_command>
 
     <command detect_errors="exit_code"><![CDATA[
@@ -82,7 +83,7 @@
 -l '$adv.lfc'
 -p '$adv.pVal'
 -d '$adv.pAdjust'
--v '$adv.volgenes'
+-G '$adv.topgenes'
 #if $adv.treat:
     -T
 #end if
@@ -277,9 +278,9 @@
             <param name="treat" type="boolean" truevalue="1" falsevalue="0" checked="False"
                 label="Test significance relative to a fold-change threshold (TREAT)"
                 help="If you want to apply a cut-off on a fold change the TREAT function can be used, see Help section below. Default: No"/>
-            <param name="volgenes" type="integer" value="10" min="0"
-                label="Number of genes to highlight in Volcano plot"
-                help="The top DE genes will be highlighted in the Volcano plot for each contrast. Default: 10."/>
+            <param name="topgenes" type="integer" value="10" min="0"
+                label="Number of genes to highlight in Volcano plot and Heatmap"
+                help="The top DE genes will be highlighted in the Volcano plot for each contrast and output in a heatmap PDF. Default: 10."/>
             <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
                 <option value="TMM" selected="true">TMM</option>
                 <option value="RLE">RLE</option>
@@ -317,6 +318,7 @@
                 <param name="contrast" value="WT-Mut" />
             </repeat>
             <param name="normalisationOption" value="TMM" />
+            <param name="topgenes" value="6" />
             <output_collection name="outTables" count="2">
                 <element name="limma-voom_Mut-WT" ftype="tabular" >
                     <assert_contents>
@@ -352,6 +354,7 @@
                 <param name="contrast" value="Mut-WT" />
             </repeat>
             <param name="normalisationOption" value="TMM" />
+            <param name="topgenes" value="6" />
             <output_collection name="outTables" count="1">
                 <element name="limma-voom_Mut-WT" ftype="tabular" >
                     <assert_contents>
@@ -375,6 +378,7 @@
                 <param name="contrast" value="Mut-WT" />
             </repeat>
             <param name="normalisationOption" value="TMM" />
+            <param name="topgenes" value="6" />
             <output name="outReport" >
                 <assert_contents>
                     <has_text text="RData" />
@@ -398,6 +402,7 @@
                 <param name="contrast" value="Mut-WT" />
             </repeat>
             <param name="normalisationOption" value="TMM" />
+            <param name="topgenes" value="6" />
             <output_collection name="outTables" count="1" >
                 <element name="limma-voom_Mut-WT" ftype="tabular" >
                     <assert_contents>
@@ -417,6 +422,7 @@
                 <param name="contrast" value="Mut-WT" />
             </repeat>
             <param name="normalisationOption" value="TMM" />
+            <param name="topgenes" value="6" />
             <output_collection name="outTables" count="1">
                 <element name="limma-voom_Mut-WT" ftype="tabular" >
                     <assert_contents>
@@ -439,6 +445,7 @@
                 <param name="contrast" value="Mut-WT" />
             </repeat>
             <param name="normalisationOption" value="TMM" />
+            <param name="topgenes" value="6" />
             <output_collection name="outTables" count="2">
                 <element name="limma-voom_Mut-WT" ftype="tabular" >
                     <assert_contents>
@@ -491,6 +498,7 @@
             <repeat name="rep_contrast">
                 <param name="contrast" value="WT-Mut" />
             </repeat>
+            <param name="topgenes" value="6" />
             <param name="normCounts" value="true" />
             <output_collection name="outTables" count="3">
                 <element name="limma-voom_Mut-WT" ftype="tabular" >
@@ -525,6 +533,7 @@
                 <param name="contrast" value="Mut-WT" />
             </repeat>
             <param name="normalisationOption" value="TMM" />
+            <param name="topgenes" value="6" />
             <param name="de_select" value="trend" />
             <param name="rdaOption" value="true" />
             <output name="outReport" >
@@ -555,6 +564,7 @@
                 <param name="contrast" value="Mut-WT" />
             </repeat>
             <param name="normalisationOption" value="TMM" />
+            <param name="topgenes" value="6" />
             <param name="de_select" value="trend" />
             <param name="rdaOption" value="true" />
             <output name="outReport" >