From e9e004cf277e1c759712a0b2bfee545637a28bf4 Mon Sep 17 00:00:00 2001
From: mthang <m.thang@qfab.org>
Date: Thu, 1 Aug 2024 22:22:47 +1000
Subject: [PATCH] patch combined_kreports.xml (#6182)
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* patch combined_kreports.xml

* insert assert_contents into test 3

* use asserts for combine_kreports.xml

* Update combine_kreports.xml

---------

Co-authored-by: mthang <mthang@qfab.org>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/krakentools/combine_kreports.xml | 37 +++++++++++++++++++++-----
 1 file changed, 31 insertions(+), 6 deletions(-)

diff --git a/tools/krakentools/combine_kreports.xml b/tools/krakentools/combine_kreports.xml
index 80a50bd162c..138f30af544 100644
--- a/tools/krakentools/combine_kreports.xml
+++ b/tools/krakentools/combine_kreports.xml
@@ -1,4 +1,4 @@
-<tool id="krakentools_combine_kreports" name="Krakentools: Combine multiple Kraken reports" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="krakentools_combine_kreports" name="Krakentools: Combine multiple Kraken reports" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>into a combined report file</description>
     <macros>
         <import>macros.xml</import>
@@ -7,12 +7,24 @@
     <expand macro="requirements"/>
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
-combine_kreports.py 
-    --reports
-    #for $report in $reports 
-        '$report' 
+#if $display_headers:
+    #for $report in $reports
+        ln -s '$report' '${report.element_identifier}' &&
     #end for
-    --output '$output' 
+#end if
+
+combine_kreports.py 	
+    --reports
+    #if $display_headers:
+        #for $report in $reports
+            '${report.element_identifier}'
+        #end for
+    #else:
+        #for $report in $reports
+            '${report}'
+        #end for
+    #end if
+    --output '$output'
     $display_headers
     $only_combined
     ]]></command>
@@ -35,6 +47,19 @@ combine_kreports.py
             <param name="display_headers" value="--no-headers"/>
             <param name="only_combined" value="--only-combined"/>
             <output name="output" file="only_combined_count.tabular"/>
+    	</test>
+        <test>
+            <param name="reports" value="beta_kreport_1.tabular,beta_kreport_3.tabular"/>
+            <param name="display_headers" value="--display-headers"/>
+            <param name="only_combined" value="--only-combined"/>
+	    <output name="output">
+		 <assert_contents>
+		      <has_text text="#Number of Samples:"/>
+		      <has_text text="#S1"/>
+		      <has_text text="#S2"/>
+		      <has_text text="#perc"/>
+		 </assert_contents>
+	    </output>
         </test>
     </tests>
     <help><![CDATA[