# HG changeset patch
# User proteore
# Date 1545062704 18000
# Node ID 36c97ab06d407ecc7dd39504a0d0d7ee3b3e71fa
# Parent  e7ff74898133fe090d809977e3bb0d78c4fb2b79
planemo upload commit c7db932b9ebeb5f9dc8ddac5fd87417ca30e8a80

diff -r e7ff74898133 -r 36c97ab06d40 topGO.xml
--- a/topGO.xml	Tue Nov 06 09:02:00 2018 -0500
+++ b/topGO.xml	Mon Dec 17 11:05:04 2018 -0500
@@ -1,5 +1,5 @@
-<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2018.10.29.2">
-    <description>(Human, Mouse, Rat) (topGO)</description>
+<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2018.12.17">
+    <description>(Human, Mouse, Rat)[topGO]</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>
         <requirement type="package" version="3.0.0">r-ggplot2</requirement>
@@ -33,9 +33,8 @@
   --option='$option'
   --threshold='$threshold'
   --correction='$correction'
-  --textoutput='$textoutput'
-  --barplotoutput='$barplot'
-  --dotplotoutput='$dotplot'
+  --textoutput='true'
+  --plot='$plot'
   --geneuniverse='$geneuniverse' 
   --background="$background_genes.background"
 
@@ -52,12 +51,12 @@
 
     <inputs>
   <conditional name="inputtype">
-    <param name="filetype" type="select" label="Select your type of input file" help="The identifiers must be Ensembl gene IDs (e.g : ENSG00000139618). If it is not the case, please use the ID Converter tool.">
-      <option value="file" selected="true">Input file containing your identifiers</option>
+    <param name="filetype" type="select" label="Enter your IDs (Ensembl Gene only)" help="Copy/paste or from a file">
+      <option value="file" selected="true">Input file containing your IDs</option>
       <option value="copy_paste">Copy/paste your list of IDs</option> 
     </param>
     <when value="copy_paste">
-      <param name="genelist" type="text" label="Enter a list of identifiers">
+      <param name="genelist" type="text" label="Enter a list of IDs">
         <sanitizer>
             <valid initial="string.printable">
                 <remove value="&apos;"/>
@@ -69,21 +68,21 @@
       </param>
     </when>
     <when value="file">
-      <param name="genelist" type="data" format="txt,tabular" label="Choose an input file" help="This file must imperatively have 1 column filled with IDs consistent with the database that will be used. Please use the MappingIDs component if this is not the case."/>
-      <param name="column" type="text" label="Please specify the column where your Ensembl IDs are (e.g : Enter 'c1' for column n°1..)" value="c1"/> 
-      <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your file have a header?" /> 
+      <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
+      <param name="column" type="text" 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="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> 
     </when>
   </conditional>
   <conditional name="background_genes">
-    <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Would you like to define your own background IDs"/>
+    <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Define your own background IDs ?"/>
     <when value="true">
       <conditional name="inputtype">
-        <param name="filetype" type="select" label="Select your type of input file" help="The identifiers must be Ensembl gene IDs (e.g : ENSG00000139618). If it is not the case, please use the ID Mapping tool.">
-          <option value="file" selected="true">Input file containing your identifiers</option>
-          <option value="copy_paste">Copy/paste your list of IDs</option> 
+        <param name="filetype" type="select" label="Enter your background IDs (Ensembl gene IDs)" help="(e.g : ENSG00000139618)">
+          <option value="file" selected="true">Input file containing your background IDs</option>
+          <option value="copy_paste">Copy/paste your background IDs</option> 
         </param>
         <when value="copy_paste">
-          <param name="genelist" type="text" label="Enter a list of identifiers">
+          <param name="genelist" type="text" label="Copy/paste your background IDs" help="IDs must be separated by spaces into the form field, for example: ENSG00000139618 ENSG00000007350">
             <sanitizer>
             <valid initial="string.printable">
                 <remove value="&apos;"/>
@@ -95,36 +94,36 @@
           </param>
         </when>
         <when value="file">
-          <param name="genelist" type="data" format="txt,tabular" label="Choose an input file" help="This file must imperatively have 1 column filled with IDs consistent with the database that will be used. Please use the MappingIDs component if this is not the case."/>
-          <param name="column" type="text" label="Please specify the column where your Ensembl IDs are (e.g : Enter 'c1' for column n°1..)" value="c1"/> 
-          <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your file have a header?" /> 
+          <param name="genelist" 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="column" type="text" label="Column number of IDs" value="c1" help="For example, fill in 'c1' if it is the first column, 'c2' if it is the second column and so on"/> 
         </when>
       </conditional>
     </when>
     <when value="false"/>
   </conditional>
-    <param name="geneuniverse" type="select" label="Select a specie">
+    <param name="geneuniverse" type="select" label="Species">
       <!--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>
-      <option value="org.Rn.eg.db" >Rat (R. norvegicus)</option>
+      <option value="org.Hs.eg.db" selected="true">Human (Homo sapiens)</option>
+      <option value="org.Mm.eg.db" >Mouse (Mouse musculus)</option>
+      <option value="org.Rn.eg.db" >Rat (Rattus norvegicus)</option>
       <!--option value="org.Sc.sgd.db" >Yeast (S. cerevisiae)</option-->
     </param>
-    <param name="ontocat" type="select" label="Ontology category">
+    <param name="ontocat" type="select" label="GO terms category">
       <option value="BP" >Biological Process</option>
       <option value="CC" >Cellular Component</option>
       <option value="MF" >Molecular Function</option>
     </param>
-    <param name="option" type="select" label="Choose the topGO option for your analysis">
+    <param name="option" type="select" label="Select the topGO parameter (see user doc)">
       <option value="classic" >Classic fisher test</option>
       <option value="elim" selected="true">Elim</option>
       <option value="weight01" >Weight01</option>
       <option value="parentchild" >ParentChild</option>
     </param>
-    <param name="threshold" type="text" label="Enter the p-value threshold level under the form 1e-level wanted (e.g : 1e-3)" value="1e-3"/>
-	  <param name="correction" label="Choose a correction for multiple testing" type="select">
+    <param name="threshold" type="text" label="p-value threshold (e.g : 1e-3)" value="1e-3"/>
+	  <param name="correction" label="Multiple testing procedure (p-value adjustment)" type="select">
       <option value="none" >None</option>
       <option value="holm">Holm correction</option>
       <option value="hochberg" >Hochberg correction</option>
@@ -134,9 +133,11 @@
       <option value="BY" >Benjamini and Yekutieli</option>
       <option value="fdr" >FDR</option>
     </param>
-    <param name="textoutput" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a text file for results" />
-    <param name="barplot" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a barplot of over-represented GO terms" />
-    <param name="dotplot" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a dotplot of over-represented GO terms" />
+    <!--param name="textoutput" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate a text file for results" /-->
+    <param name="plot" type="select" display="checkboxes" multiple="true" label="Graphical display" optional="false">
+      <option selected = "true" value="dotplot">dot-plot</option>
+      <option value="barplot">bar-plot</option>
+    </param>
     </inputs>
     <outputs>
 
@@ -183,8 +184,8 @@
    <help><![CDATA[
       
       
-**Galaxy component based on R package topGO.** 
-
+**Description**
+This tool is based on R package topGO. topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be applied.
 **Input required**
 
 This component works with Ensembl gene ids (e.g : ENSG0000013618). You can
diff -r e7ff74898133 -r 36c97ab06d40 topGO_enrichment.R
--- a/topGO_enrichment.R	Tue Nov 06 09:02:00 2018 -0500
+++ b/topGO_enrichment.R	Mon Dec 17 11:05:04 2018 -0500
@@ -24,8 +24,7 @@
       --correction
       --threshold
       --text
-      --barplot
-      --dotplot
+      --plot
       --column
       --geneuniverse
       --header
@@ -296,8 +295,8 @@
 correction = args$correction
 threshold = as.numeric(args$threshold)
 text = str2bool(args$textoutput)
-barplot = str2bool(args$barplotoutput)
-dotplot = str2bool(args$dotplotoutput)
+barplot = "barplot" %in% unlist(strsplit(args$plot,","))
+dotplot = "dotplot" %in% unlist(strsplit(args$plot,","))
 column = as.numeric(gsub("c","",args$column))
 geneuniverse = args$geneuniverse
 header = str2bool(args$header)