diff topGO.xml @ 11:fa2e27165d5d draft

planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty

--- a/topGO.xml	Tue Dec 18 10:06:00 2018 -0500
+++ b/topGO.xml	Mon Mar 04 08:37:49 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2018.12.17">
+<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.02.19">
     <description>(Human, Mouse, Rat)[topGO]</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>
@@ -69,7 +69,9 @@
     </when>
     <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"/> 
+      <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> 
+      </param>
       <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> 
     </when>
   </conditional>
@@ -96,7 +98,9 @@
         <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="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"/> 
+          <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> 
         </when>
       </conditional>
     </when>
@@ -141,16 +145,16 @@
     </inputs>
     <outputs>
 
-      <data name="outputtext" format="tsv" label="Text output for topGO analysis $ontocat category" from_work_dir="result">
-        <filter>textoutput</filter>
+      <data name="outputtext" format="tsv" label="Text output for topGO analysis $ontocat category" from_work_dir="result.tsv">
+        <!--filter>textoutput</filter-->
+      </data>
+
+      <data name="outputdotplot" format="png" label="Dotplot output for topGO analysis $ontocat category" from_work_dir="dotplot.png">
+        <filter>'dotplot' in plot</filter>
       </data>
 
       <data name="outputbarplot" format="png" label="Barplot output for topGO analysis $ontocat category" from_work_dir="barplot.png">
-        <filter>barplot</filter>
-      </data>
-      
-      <data name="outputdotplot" format="png" label="Dotplot output for topGO analysis $ontocat category" from_work_dir="dotplot.png">
-        <filter>dotplot</filter>
+        <filter>'barplot' in plot</filter>
       </data>
       
    </outputs>