# HG changeset patch
# User sigven
# Date 1693237374 0
# Node ID 023155e2e66c5701a244d33bd656722f44c864cb
# Parent  60dde5746a5e4da8880edcad046efe19d74cea73
Uploaded

diff -r 60dde5746a5e -r 023155e2e66c oncoenrichr_wrapper.xml
--- a/oncoenrichr_wrapper.xml	Mon Aug 14 23:49:08 2023 +0000
+++ b/oncoenrichr_wrapper.xml	Mon Aug 28 15:42:54 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="oncoenrichr_wrapper" name="oncoEnrichR" version="1.4.2">
+<tool id="oncoenrichr_wrapper" name="oncoEnrichR" version="1.4.2.1">
   <description>Cancer-dedicated gene set interpretation</description>
     <requirements>
         <container type="docker">sigven/oncoenrichr:1.4.2</container>
@@ -27,7 +27,7 @@
 
       R -e 'suppressPackageStartupMessages(library(oncoEnrichR));
       suppressWarnings(load(system.file("internal_db", "oedb.rda", package = "oncoEnrichR")));
-      gene_data <- read.csv("$input_file", strip.white = TRUE);
+      gene_data <- read.csv("$input_file", strip.white = TRUE, header = F);
       oe_report <- oncoEnrichR::onco_enrich(
         query = gene_data[[1]],
         oeDB = oedb,
@@ -65,7 +65,7 @@
       show_synleth = $modules.show_synleth,
 
       #if $background_file
-          bgset = read.csv("$background_file", strip.white = TRUE)[[1]],
+          bgset = read.csv("$background_file", strip.white = TRUE, header = F)[[1]],
 		#if $fun_enrich.custom_bgset.bg_enrich_id_type
             bgset_id_type = "$fun_enrich.custom_bgset.bg_enrich_id_type",
           #end if
@@ -306,7 +306,7 @@
   <help><![CDATA[
 .. class:: infomark
 
-The query gene set is limited to n = 1000 identifiers. A limited query gene set (e.g. n < 5) will in general reduce the relevance and significance of many oncoEnrichR report modules.
+The query gene set is limited to n = 1000 identifiers. **NOTE**: A minimum of two gene entries are required to run the tool. Note also that a limited query gene set (e.g. n < 5) in general reduces the relevance and significance of many oncoEnrichR report modules.
 
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