diff topGO.xml @ 9:70c0c8757f5f draft

planemo upload commit 9d3e0b226140b566fc529fd0ffe7aa9e8388c6e5-dirty

--- a/topGO.xml	Fri Mar 23 10:43:32 2018 -0400
+++ b/topGO.xml	Fri Sep 21 05:32:38 2018 -0400
@@ -1,15 +1,20 @@
-<tool id="topGO" name="topGO" version="0.1.0">
+<tool id="topGO" name="topGO" version="2018.09.21">
     <description>
     Enrichment analysis for Gene Ontology
     </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="3.4.1">bioconductor-org.hs.eg.db</requirement>
-        <requirement type="package" version="1.54.0">bioconductor-graph</requirement>
-        <requirement type="package" version="1.38.2">bioconductor-annotationdbi</requirement>
-        <requirement type="package" version="3.4.1">bioconductor-go.db</requirement>
-        <requirement type="package" version="2.28.0">bioconductor-topgo</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.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="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>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -73,7 +78,7 @@
     </when>
     <when value="file_all">
       <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 you would like to apply the comparison (e.g : Enter c1)" value="c1"/> 
+      <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="select" label="Does your file have a header?" multiple="false" optional="false"> 
  	<option value="TRUE" selected="true">Yes</option>
@@ -82,12 +87,12 @@
     </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" >C.elegans</option>
-        <option value="org.Dm.eg.db" >Fly</option>
-        <option value="org.Hs.eg.db" selected="true">Human</option>
-        <option value="org.Mm.eg.db" >Mouse</option>
-        <option value="org.Sc.sqd.db" >Yeast</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>
+        <option value="org.Sc.sgd.db" >Yeast (S. cerevisiae)</option>
       </param>
 
       <param name="ontocat" type="select" label="Ontology category">