# HG changeset patch
# User proteore
# Date 1569500744 14400
# Node ID 0bc8e48b057826159b785b511a8a02690db6becf
# Parent  79d0f1773124e758948ffad451122badcc2dc99d
planemo upload commit 072cac8e610c524081ce40bb6f3a8edcdfbdbe9c

diff -r 79d0f1773124 -r 0bc8e48b0578 topGO.xml
--- a/topGO.xml	Thu Jun 27 04:22:25 2019 -0400
+++ b/topGO.xml	Thu Sep 26 08:25:44 2019 -0400
@@ -1,26 +1,26 @@
-<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.06.27">
+<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.09.26">
     <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>
-        <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
-        <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
-        <requirement type="package" version="3.5.0">bioconductor-org.rn.eg.db</requirement>
+        <requirement type="package">R</requirement>
+        <requirement type="package">r-ggplot2</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.rn.eg.db</requirement>
         <!--requirement type="package" version="3.6.0">bioconductor-org.ce.eg.db</requirement-->
         <!--requirement type="package" version="3.6.0">bioconductor-org.dm.eg.db</requirement-->
         <!--requirement type="package" version="3.6.0">bioconductor-org.sc.sgd.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>
-        <requirement type="package" version="2.30.0">bioconductor-topgo</requirement>
+        <requirement type="package" version="1.62.0">bioconductor-graph</requirement>
+        <requirement type="package" version="1.46.0">bioconductor-annotationdbi</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-go.db</requirement>
+        <requirement type="package" version="2.36.0">bioconductor-topgo</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-       
-  Rscript --vanilla $__tool_directory__/topGO_enrichment.R 
+
+  Rscript --vanilla $__tool_directory__/topGO_enrichment.R
   --inputtype="$inputtype.filetype"
   --input='$inputtype.genelist'
 
@@ -35,7 +35,7 @@
   --correction='$correction'
   --textoutput='true'
   --plot='$plot'
-  --geneuniverse='$geneuniverse' 
+  --geneuniverse='$geneuniverse'
   --background="$background_genes.background"
 
   #if $background_genes.background == "true"
@@ -53,7 +53,7 @@
   <conditional name="inputtype">
     <param name="filetype" type="select" label="Enter your IDs (Ensembl Gene Id)" 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> 
+      <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 IDs">
@@ -70,9 +70,9 @@
     <when value="file">
       <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">
-        <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> 
+        <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
       </param>
-      <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> 
+      <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
     </when>
   </conditional>
   <conditional name="background_genes">
@@ -81,7 +81,7 @@
       <conditional name="inputtype">
         <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> 
+          <option value="copy_paste">Copy/paste your background IDs</option>
         </param>
         <when value="copy_paste">
           <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">
@@ -97,10 +97,10 @@
         </when>
         <when value="file">
           <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="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">
             <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
-          </param> 
+          </param>
         </when>
       </conditional>
     </when>
@@ -156,7 +156,7 @@
       <data name="outputbarplot" format="png" label="Barplot output for topGO analysis $ontocat category" from_work_dir="barplot.png">
         <filter>'barplot' in plot</filter>
       </data>
-      
+
    </outputs>
    <tests>
      <test>
@@ -169,7 +169,7 @@
        <param name="ontocat" value="BP"/>
        <param name="option" value="elim"/>
        <param name="threshold" value="1e-3"/>
-       <param name="correction" value="BH"/> 
+       <param name="correction" value="BH"/>
        <param name="textoutput" value="TRUE"/>
        <param name="plot" value="dotplot,barplot"/>
        <param name="geneuniverse" value="org.Hs.eg.db"/>
@@ -179,8 +179,8 @@
      </test>
    </tests>
    <help><![CDATA[
-      
-      
+
+
 **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.
@@ -192,17 +192,17 @@
 **Input required**
 
 This component works with Ensembl gene IDs (e.g : ENSG0000013618). You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab)
-and then specifying the column number that contains the ENSG IDs. 
+and then specifying the column number that contains the ENSG IDs.
 
 -----
 
 **Parameters**
 
-"Species": "Species": the three available species are Homo sapiens, Mus musculus and Rattus norvegicus 
- 
+"Species": "Species": the three available species are Homo sapiens, Mus musculus and Rattus norvegicus
+
 "GO terms category": select either Biogical Process (BP)(by default), Cellular Component (CC) or Molecular Function (MF)
- 
-"Select GO scoring method: topGO provides the commonly used Fisher test for evaluating which GO terms are over-represented in your gene/protein list; it also provides other GO scoring algorithms (i.e. Elim, Weight01, Parentchild). For the merits of each option and their algorithmic description, please refer to topGO manual: 
+
+"Select GO scoring method: topGO provides the commonly used Fisher test for evaluating which GO terms are over-represented in your gene/protein list; it also provides other GO scoring algorithms (i.e. Elim, Weight01, Parentchild). For the merits of each option and their algorithmic description, please refer to topGO manual:
 https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
 
 "p-value threshold (e.g : 1e-3)": must be in the form of "1e-5" (i.e. 0.00001)
@@ -214,29 +214,29 @@
 
 **Output**
 
-Two types of output are available: textual and/or graphical outputs (barplot and/or a dotplot (set by default)). 
+Two types of output are available: textual and/or graphical outputs (barplot and/or a dotplot (set by default)).
 
 *Textual output*
 
-The text output lists all the GO-terms that were found significantly enriched according to the specified threshold (p-value).    
+The text output lists all the GO-terms that were found significantly enriched according to the specified threshold (p-value).
 
 The different fields are as follow:
 
 - Annotated : number of genes in the selected species that are annotated with the GO-term.
 
-- Significant : number of genes belonging to your input annotated with the GO-term. 
+- Significant : number of genes belonging to your input annotated with the GO-term.
 
 - Expected : represents the expected number of interesting genes mapped to the GO term if the interesting genes were randomly distributed over all GO terms.
 
-- p-values : p-value obtained after the test 
+- p-values : p-value obtained after the test
 
-- ( q-values  : additional column with adjusted pvalues ) 
+- ( q-values  : additional column with adjusted pvalues )
 
 -----
 
 .. class:: infomark
 
-Packages used: 
+Packages used:
     - bioconductor-org.hs.eg.db v3.5.0
     - bioconductor-org.mm.eg.db v3.5.0
     - bioconductor-org.rn.eg.db v3.5.0