# HG changeset patch
# User kkonganti
# Date 1655931383 14400
# Node ID 48eebe68ec69be1600ff3402e3fcf43e2ec7937e
# Parent  00fa638e833ee3d6b327511566a33bd1e40cf6f4
"planemo upload"

diff -r 00fa638e833e -r 48eebe68ec69 centrifuge_process.xml
--- a/centrifuge_process.xml	Wed Jun 22 16:13:46 2022 -0400
+++ b/centrifuge_process.xml	Wed Jun 22 16:56:23 2022 -0400
@@ -5,7 +5,7 @@
         <requirement type="package">pandas</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        $__tool_directory__/process_centrifuge_output.py -o '$input1' -r '$input2' -b '$input3' -t '$output1'
+        $__tool_directory__/process_centrifuge_output.py -o '$input1' -r '$input2' -b '$input3' -t FAL11127.process-centrifuge-bug-ids.txt
     ]]></command>
     <inputs>
         <param type="data" name="input1" format="txt" />
@@ -13,14 +13,14 @@
 	<param type="text" name="input3" format="txt" />
     </inputs>
     <outputs>
-        <data name="output1" format="txt" />
+        <data name="output" format="txt" from_work_dir="FAL11127.process-centrifuge-bug-ids.txt" />
     </outputs>
     <tests>
         <test>
             <param name="input1" value="FAL11127.centrifuge.output.txt"/>
 	    <param name="input2" value="FAL11127.centrifuge.report.txt"/>
 	    <param name="input3" value="Escherichia coli"/>
-            <output name="output1" file="FAL11127.process-centrifuge-bug-ids.txt"/>
+            <output name="output" file="FAL11127.process-centrifuge-bug-ids.txt"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r 00fa638e833e -r 48eebe68ec69 process_centrifuge_output.py
--- a/process_centrifuge_output.py	Wed Jun 22 16:13:46 2022 -0400
+++ b/process_centrifuge_output.py	Wed Jun 22 16:56:23 2022 -0400
@@ -11,7 +11,7 @@
 def main():
     # READ IN ARGUMENTS
     desc = """
-    This script is part of the centriflaken pipeline: It processes centrifuge
+    This script is part of the CPIPES - centriflaken pipeline: It processes centrifuge
     output and produces either a filtered FASTQ or a text file of FASTQ IDs based
     on the supplied taxa/bug
     """
@@ -72,4 +72,4 @@
     TF.close()
 
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()