diff bbduk.xml @ 1:60dd895841cd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"

--- a/bbduk.xml	Thu Nov 11 16:38:32 2021 +0000
+++ b/bbduk.xml	Tue Feb 01 23:00:44 2022 +0000
@@ -10,18 +10,16 @@
 
 #if str($input_type_cond.input_type) in ['single', 'pair']:
     #set read1 = $input_type_cond.read1
-    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
     ## bbduk uses the file extension to determine the input format.
-    #set ext = $read1_identifier + '.fastq'
+    #set ext = '.fastq'
     #if $read1.ext.endswith('.gz'):
         #set ext = $ext + '.gz'
     #end if
-    #set read1_file = $read1_identifier + $ext
+    #set read1_file = 'forward'  + $ext
     ln -s '${read1}' '${read1_file}' &&
     #if str($input_type_cond.input_type) == 'pair':
         #set read2 = $input_type_cond.read2
-        #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
-        #set read2_file = $read2_identifier + $ext
+        #set read2_file = 'reverse' + $ext
         ln -s '${read2}' '${read2_file}' &&
     #end if
 #else:
@@ -231,17 +229,17 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Unmatched)">
+        <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)">
             <filter>str(outputs_select).find('outu') >= 0</filter>
             <filter>'outu' in outputs_select</filter>
         </data>
-        <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Unmatched)">
+        <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Unmatched)">
             <filter>'outu' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
         </data>
-        <data name="outputm" format="fastqsanger" label="${tool.name} on ${on_string} (Matched)">
+        <data name="outputm" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Matched)">
             <filter>'outm' in outputs_select</filter>
         </data>
-        <data name="outputm2" format="fastqsanger" label="${tool.name} on ${on_string} (Matched)">
+        <data name="outputm2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Matched)">
             <filter>'outm' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
         </data>
         <data name="outputs" format="fastqsanger" label="${tool.name} on ${on_string} (Single)">