Mercurial > repos > proteore > proteore_clusterprofiler

changeset 20:a91d407e1938 draft

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planemo upload commit d636fd65b39353cbb29228d309235f3a6db37568-dirty
author proteore
date Wed, 03 Oct 2018 04:08:59 -0400
parents 7b3eb5767497
children d72690c9d928
files GO-enrich.R cluster_profiler.xml
diffstat 2 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/GO-enrich.R	Fri Sep 28 05:02:31 2018 -0400
+++ b/GO-enrich.R	Wed Oct 03 04:08:59 2018 -0400
@@ -260,13 +260,13 @@
   for (onto in ontology) {
     if (args$go_represent == "true") {
       ggo<-repartition.GO(gene, orgdb, onto, level, readable=TRUE)
-      output_path = paste("cluster_profiler_GGO_",onto,".csv",sep="")
+      output_path = paste("cluster_profiler_GGO_",onto,".tsv",sep="")
       write.table(ggo, output_path, sep="\t", row.names = FALSE, quote=FALSE)
     }
 
     if (args$go_enrich == "true") {
       ego<-enrich.GO(gene, universe_gene, orgdb, onto, pval_cutoff, qval_cutoff,plot)
-      output_path = paste("cluster_profiler_EGO_",onto,".csv",sep="")
+      output_path = paste("cluster_profiler_EGO_",onto,".tsv",sep="")
       write.table(ego, output_path, sep="\t", row.names = FALSE, quote=FALSE)
     }
   }
--- a/cluster_profiler.xml	Fri Sep 28 05:02:31 2018 -0400
+++ b/cluster_profiler.xml	Wed Oct 03 04:08:59 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="cluter_profiler" name="clusterProfiler" version="2018.09.28.2">
+<tool id="cluter_profiler" name="clusterProfiler" version="2018.10.03">
     <description>
     GO terms classification and enrichment analysis
     </description>
@@ -167,7 +167,7 @@
     <outputs>
         <data name="log" format="tabular" label="Cluster profiler" />
         <collection type="list" label="clusterProfiler text files" name="text_output">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+\.csv)" ext="csv"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+\.tsv)" ext="tsv"/>
         </collection>
         <collection type="list" label="clusterProfiler diagram outputs" name="graph_output" >
 	        <discover_datasets pattern="(?P&lt;designation&gt;.+plot)" ext="png" />