From 05f18d029bb1308ab37e575f6972e8e18792e8b5 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 23 Aug 2018 11:16:28 +0200
Subject: [PATCH] Fix linkToGProfile test

---
 tools/phenotype_association/linkToGProfile.pl  |  2 +-
 tools/phenotype_association/linkToGProfile.xml | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/tools/phenotype_association/linkToGProfile.pl b/tools/phenotype_association/linkToGProfile.pl
index 0f0ee242e09..2d6e8100482 100755
--- a/tools/phenotype_association/linkToGProfile.pl
+++ b/tools/phenotype_association/linkToGProfile.pl
@@ -77,7 +77,7 @@ if (@pos) { $params{"region_query"} = 1; }
 
 open(FH, ">", $out) or die "Couldn't open $out, $!\n";
 print FH "<html><head><title>g:Profiler link</title></head><body>\n";
-print FH '<form method="POST" action="http://biit.cs.ut.ee/gprofiler/index.cgi">';
+print FH '<form method="POST" action="http://biit.cs.ut.ee/gprofiler/index.cgi">', "\n";
 foreach my $k (keys %params) {
    print FH "<input type='hidden' name='$k' value='$params{$k}'>\n";
 }
diff --git a/tools/phenotype_association/linkToGProfile.xml b/tools/phenotype_association/linkToGProfile.xml
index a21a00d3c8c..908099e8270 100644
--- a/tools/phenotype_association/linkToGProfile.xml
+++ b/tools/phenotype_association/linkToGProfile.xml
@@ -1,8 +1,8 @@
 <tool id="hgv_linkToGProfile" name="g:Profiler" version="1.0.0">
   <description>tools for functional profiling of gene lists</description>
 
-  <command interpreter="perl">
-    linkToGProfile.pl $input $type $out_file1 -region=$region -gene=$genes -chr=${input.metadata.chromCol} -start=${input.metadata.startCol} -end=${input.metadata.endCol}
+  <command detect_errors="exit_code">
+perl '$__tool_directory__/linkToGProfile.pl' '$input' $type '$out_file1' -region='$region' -gene=$genes -chr=${input.metadata.chromCol} -start=${input.metadata.startCol} -end=${input.metadata.endCol}
   </command>
 
   <inputs>
@@ -34,10 +34,10 @@
 
   <tests>
     <test>
-      <param name="input" ftype="tabular" value="linkToGProfile.tabular" />
+      <param name="input" ftype="bed" value="linkToGProfile.tabular" />
       <param name="genes" value="2" />
-      <param name="type" value="ENTREZGENE_ACC" />
-      <output name="out_file1" file="linkToGProfile_1.out" />
+      <param name="type" value="Entrez Gene Acc" />
+      <output name="out_file1" file="linkToGProfile_1.out" sort="true"/>
     </test>
   </tests>