Mercurial > repos > proteore > proteore_topgo

diff topGO.xml @ 2:f62d29616966 draft

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planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
author proteore
date Tue, 27 Feb 2018 09:09:42 -0500
parents 6788a57c5cb5
children 5f6d95716bc9
line wrap: on
line diff
--- a/topGO.xml	Fri Feb 16 04:15:08 2018 -0500
+++ b/topGO.xml	Tue Feb 27 09:09:42 2018 -0500
@@ -3,6 +3,8 @@
     performs enrichment analysis using R package topGO
     </description>
     <requirements>
+        <requirement type="package" version="3.4.1">R</requirement>
+        <requirement type="package" version="2.2.1">r-ggplot2</requirement>
         <requirement type="package" version="1.54.0">bioconductor-graph</requirement>
         <requirement type="package" version="2.28.0">bioconductor-topgo</requirement>
     </requirements>
@@ -12,13 +14,36 @@
     <command><![CDATA[
     
   #if $inputtype.filetype == "file_all": 
-  Rscript --vanilla $__tool_directory__/enrichment_v3.R --inputtype tabfile --input '$inputtype.genelist' --ontology '$ontocat' --option '$option' --threshold '$threshold' --correction '$correction' --textoutput '$condtext.textoutput' --barplotoutput '$condbar.barplotoutput' --dotplotoutput '$conddot.dotplotoutput' --column '$inputtype.column' --geneuniverse '$geneuniverse' --header '$inputtype.header'
+  Rscript --vanilla $__tool_directory__/enrichment_v3.R 
+  --inputtype tabfile 
+  --input '$inputtype.genelist' 
+  --ontology '$ontocat' 
+  --option '$option' 
+  --threshold '$threshold' 
+  --correction '$correction' 
+  --textoutput '$condtext.textoutput' 
+  --barplotoutput '$condbar.barplotoutput' 
+  --dotplotoutput '$conddot.dotplotoutput' 
+  --column '$inputtype.column' 
+  --geneuniverse '$geneuniverse' 
+  --header '$inputtype.header'
   #end if
     
     
-      #if $inputtype.filetype == "copy_paste": 
-  Rscript --vanilla $__tool_directory__/enrichment_v3.R --inputtype copypaste --input '$inputtype.genelist' --ontology '$ontocat' --option '$option' --threshold '$threshold' --correction '$correction' --textoutput '$condtext.textoutput' --barplotoutput '$condbar.barplotoutput' --dotplotoutput '$conddot.dotplotoutput' --column c1 --geneuniverse '$geneuniverse' --header None
-
+  #if $inputtype.filetype == "copy_paste": 
+  Rscript --vanilla $__tool_directory__/enrichment_v3.R 
+  --inputtype copypaste 
+  --input '$inputtype.genelist' 
+  --ontology '$ontocat' 
+  --option '$option' 
+  --threshold '$threshold' 
+  --correction '$correction' 
+  --textoutput '$condtext.textoutput' 
+  --barplotoutput '$condbar.barplotoutput' 
+  --dotplotoutput '$conddot.dotplotoutput' 
+  --column c1 
+  --geneuniverse '$geneuniverse' 
+  --header None
   #end if