# HG changeset patch
# User proteore
# Date 1550507159 18000
# Node ID f2c0a2b448410be0eed655fb11938ef80d1a67fa
# Parent  b62fd03a3822fb11d7ed3279a3caa9fcb53fd34e
planemo upload commit bfee528de437dc698b227a274983af3f3106cbb3-dirty

diff -r b62fd03a3822 -r f2c0a2b44841 GO-enrich.R
--- a/GO-enrich.R	Fri Dec 21 03:55:25 2018 -0500
+++ b/GO-enrich.R	Mon Feb 18 11:25:59 2019 -0500
@@ -156,9 +156,12 @@
   #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
   #load("/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
   
-  plot = unlist(strsplit(args$plot,","))
+  
   go_represent=str2bool(args$go_represent)
   go_enrich=str2bool(args$go_enrich)
+  if (go_enrich){
+    plot = unlist(strsplit(args$plot,","))
+  }
   
   suppressMessages(library(args$species, character.only = TRUE, quietly = TRUE))
   
diff -r b62fd03a3822 -r f2c0a2b44841 cluster_profiler.xml
--- a/cluster_profiler.xml	Fri Dec 21 03:55:25 2018 -0500
+++ b/cluster_profiler.xml	Mon Feb 18 11:25:59 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2018.12.21">
+<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2019.02.18">
     <description>(Human, Mouse, Rat)[clusterProfiler]</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>
@@ -32,6 +32,7 @@
         #end if
 
         #if $ego.go_enrich == "true"
+            --plot="$ego.plot" 
             --go_enrich="true"
             --pval_cutoff="$ego.pval"
             --qval_cutoff="$ego.qval"
@@ -51,7 +52,6 @@
             --go_enrich="false"
         #end if
         
-        --plot="$ego.plot"        
         --onto_opt="$ontology" > $log
     ]]></command>
     <inputs>
@@ -75,7 +75,9 @@
             <when value="file" >
                 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
                 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
-                <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
+                <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
+                    <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
+                </param>
             </when>
         </conditional>
         <conditional name="idti" >
@@ -135,7 +137,9 @@
                             <when value="file" >
                                 <param name="file" type="data" format="txt,tabular" label="Select file that contains your background IDs list" help="" />
                                 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
-                                <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
+                                <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
+                                    <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
+                                </param>
                             </when>
                         </conditional>
                         <conditional name="universe_idti" >