# HG changeset patch
# User iuc
# Date 1722527208 0
# Node ID 4960abe31b4d80553ed7b285678da5dfcb6925f1
# Parent  073c867c5244140635df37093833e7d35277b943
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit b57c22bb6ff8bbc2730c909713689311be4c3eaa

diff -r 073c867c5244 -r 4960abe31b4d combine_kreports.xml
--- a/combine_kreports.xml	Tue Jun 20 20:03:51 2023 +0000
+++ b/combine_kreports.xml	Thu Aug 01 15:46:48 2024 +0000
@@ -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 
+#if $display_headers:
+    #for $report in $reports
+        ln -s '$report' '${report.element_identifier}' &&
+    #end for
+#end if
+
+combine_kreports.py 	
     --reports
-    #for $report in $reports 
-        '$report' 
-    #end for
-    --output '$output' 
+    #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 @@
             <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[