diff samtools_mpileup.xml @ 10:8da515fbc1bf draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit a18f79e7cfe15fd6e1a5f70533616c379e4e7c6a"

--- a/samtools_mpileup.xml	Mon Sep 03 13:10:02 2018 -0400
+++ b/samtools_mpileup.xml	Tue Sep 21 09:33:51 2021 +0000
@@ -12,16 +12,15 @@
     @PREPARE_IDX_MULTIPLE@
 
     #if $reference_source.reference_source_selector == "history":
-        ln -s '${reference_source.ref_file}' &&
-        samtools faidx `basename '${reference_source.ref_file}'` &&
+        #set ref_fa = 'ref.fa'
+        ln -s '${reference_source.ref_file}' 'ref.fa' &&
+        samtools faidx ref.fa &&
+    #else:
+        #set ref_fa = str( $reference_source.ref_file.fields.path )
     #end if
 
     samtools mpileup
-    #if $reference_source.reference_source_selector != "history":
-        -f '${reference_source.ref_file.fields.path}'
-    #else:
-        -f '${reference_source.ref_file}'
-    #end if
+        -f '$ref_fa'
     #for $i in range(len( $input_bams )):
         '${i}'
     #end for