Mercurial > repos > proteore > proteore_topgo

changeset 8:f325701409e6 draft

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planemo upload commit 2007526ffd7115f74961cddf477086e43d0726a5
author proteore
date Wed, 19 Sep 2018 09:23:51 -0400
parents 8d35400e0325
children 8f5025a35a84
files enrichment_v3.R topGO.xml
diffstat 2 files changed, 5 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/enrichment_v3.R	Wed Sep 19 08:51:27 2018 -0400
+++ b/enrichment_v3.R	Wed Sep 19 09:23:51 2018 -0400
@@ -63,6 +63,7 @@
 
 
 # Parse command line arguments
+
 args = commandArgs(trailingOnly = TRUE)
 
 # create a list of the arguments from the command line, separated by a blank space
@@ -87,9 +88,6 @@
     stop("Not enough/Too many arguments", call. = FALSE)
 }
 
-#save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/topGO/args.Rda")
-#load("/home/dchristiany/proteore_project/ProteoRE/tools/topGO/args.Rda")
-
 typeinput = options.args[1]
 listfile = options.args[2]
 onto = as.character(options.args[3])
--- a/topGO.xml	Wed Sep 19 08:51:27 2018 -0400
+++ b/topGO.xml	Wed Sep 19 09:23:51 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="topGO" name="topGO" version="2018.09.18.2">
+<tool id="topGO" name="topGO" version="2018.09.19">
     <description>
     Enrichment analysis for Gene Ontology
     </description>
@@ -10,7 +10,7 @@
         <requirement type="package" version="3.5.0">bioconductor-org.ce.eg.db</requirement>
         <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement>
         <requirement type="package" version="3.5.0">bioconductor-org.sc.sgd.db</requirement>
-        <requirement type="package" version="3.5.0">bioconductor-org.at.tair.db</requirement>
+        <!--requirement type="package" version="3.5.0">bioconductor-org.at.tair.db</requirement-->
         <requirement type="package" version="1.56.0">bioconductor-graph</requirement>
         <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement>
         <requirement type="package" version="3.5.0">bioconductor-go.db</requirement>
@@ -87,8 +87,8 @@
     </when>
   </conditional>
       <param name="geneuniverse" type="select" label="Select a specie">
-        <option value="org.At.tair.db" >Arabidopsis</option>
-        <option value="org.Ce.eg.db" >Worm (C.elegans)</option>
+        <!--option value="org.At.tair.db" >Arabidopsis</option-->
+        <option value="org.Ce.eg.db" >Worm (C. elegans)</option>
         <option value="org.Dm.eg.db" >Fly (D. melanogaster)</option>
         <option value="org.Hs.eg.db" selected="true">Human (H. sapiens)</option>
         <option value="org.Mm.eg.db" >Mouse (M. musculus)</option>