# HG changeset patch
# User maciek
# Date 1757598700 0
# Node ID 1eac4316c2427648b965883d7c1aa4f0b2132cd0
# Parent  61a5641ab89b13965e6d4cd5e8181720d4b6c9ed
Uploaded

diff -r 61a5641ab89b -r 1eac4316c242 fbqs_integrator/fbqs_integrator.xml
--- a/fbqs_integrator/fbqs_integrator.xml	Mon Jul 14 06:51:12 2025 +0000
+++ b/fbqs_integrator/fbqs_integrator.xml	Thu Sep 11 13:51:40 2025 +0000
@@ -9,25 +9,26 @@
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/fbqs-integrator.py'
+    python '$__tool_directory__/fbqs-integrator.py'
         --staramr '$staramr'
         --fastp-jsons
-        #for $file in $fastp_jsons
-            '$file'
+        #for $input in $fastp_jsons:
+            '$input'
         #end for
-        --quast-files
-        #for $file in $quast_files
-            '$file'
+        --quast-files  
+        #for $input in $quast_files:
+            '$input'
         #end for
-        #if $bracken_jsons
-        --bracken-jsons
-        #for $file in $bracken_jsons
-            '$file'
-        #end for
+        #if $bracken_jsons:
+            --bracken-jsons
+            #for $input in $bracken_jsons:
+                '$input'
+            #end for
         #end if
-        --output '$output'
+        --output results.xlsx
     ]]></command>
 
+
     <inputs>
         <param name="staramr" type="data" format="xlsx" label="Input STARAMR report (.xlsx)" 
                help="STARAMR Excel report from upstream workflow"/>
@@ -43,9 +44,15 @@
     </inputs>
 
     <outputs>
-        <data name="output" format="xlsx" label="Enhanced STARAMR report"/>
+        <data 
+            format="xlsx" 
+            name="enhanced_report" 
+            from_work_dir="results.xlsx" 
+            label="${tool.name} on ${on_string}: Enhanced STARAMR Report">
+        </data>
     </outputs>
 
+
     <help><![CDATA[
 **What it does**
 
@@ -78,4 +85,4 @@
 }
         </citation>
     </citations>
-</tool>
+</tool>
\ No newline at end of file