Mercurial > repos > proteore > proteore_clusterprofiler

changeset 22:6dafa28110f5 draft

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planemo upload commit f9fa23f3f9cefa5c4a3dc06686add83a23c17ad0-dirty
author proteore
date Thu, 04 Oct 2018 09:25:39 -0400
parents d72690c9d928
children 879367568ea6
files GO-enrich.R cluster_profiler.xml
diffstat 2 files changed, 7 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/GO-enrich.R	Wed Oct 03 04:19:18 2018 -0400
+++ b/GO-enrich.R	Thu Oct 04 09:25:39 2018 -0400
@@ -182,7 +182,7 @@
     # Get file content
     file = readfile(filename, header)
     # Extract Protein IDs list
-    input =  sapply(as.character(file[,ncol]),function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE)
+    input =  unlist(sapply(as.character(file[,ncol]),function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE))
   }
   id_type = args$id_type
   ## Get input gene list from input IDs
--- a/cluster_profiler.xml	Wed Oct 03 04:19:18 2018 -0400
+++ b/cluster_profiler.xml	Thu Oct 04 09:25:39 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="cluter_profiler" name="clusterProfiler" version="2018.10.03.2">
+<tool id="cluter_profiler" name="clusterProfiler" version="2018.10.04">
     <description>
     GO terms classification and enrichment analysis
     </description>
@@ -53,7 +53,7 @@
             --go_enrich="false"
         #end if
         
-        --plot="$plot"        
+        --plot="$ego.plot"        
         --onto_opt="$ontology" > $log
     ]]></command>
     <inputs>
@@ -147,6 +147,10 @@
                     </when>
                     <when value="false"/>
                 </conditional>
+                <param name="plot" type="select" display="checkboxes" multiple="true" label="Please select your visualization for enrichment analysis" optional="false">
+                    <option selected = "true" value="dotplot">dot-plot</option>
+                    <option value="barplot">bar-plot</option>
+        </param>
             </when>
             <when value="false"/>
         </conditional>
@@ -157,11 +161,6 @@
             <option value="MF">Molecular Function</option>
         </param>
 	    
-	    <param name="plot" type="select" display="checkboxes" multiple="true" label="Please select your visualization for enrichment analysis" optional="false">
-            <option selected = "true" value="dotplot">dot-plot</option>
-            <option value="barplot">bar-plot</option>
-        </param>
-	    
     </inputs>
     <outputs>
         <data name="log" format="tabular" label="Cluster profiler" />