Mercurial > repos > iuc > hal_maf2hal

diff hal_maf2hal.xml @ 1:8af265f90d58 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit f46096b336bf460424143fc9d633b5e7c20bf1cf
author iuc
date Thu, 05 Mar 2026 11:32:14 +0000
parents 0cfe56c4ac68
children
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--- a/hal_maf2hal.xml	Fri Feb 06 10:45:54 2026 +0000
+++ b/hal_maf2hal.xml	Thu Mar 05 11:32:14 2026 +0000
@@ -12,12 +12,12 @@
             cp '$mode.input_hal' writable_hal.hal && 
         #end if
         ## Uncompress input
-        #if $input_maf.ext.endswith('.gz'):
+        #if $input_maf.is_of_type('maf.gz'):
             gunzip -c '$input_maf' > uncompressed_input.maf &&
-        #else if $input_maf.ext.endswith('.bz2'):
+        #else if $input_maf.is_of_type('maf.bz2'):
             bunzip2 -c '$input_maf' > uncompressed_input.maf &&
         #else
-            cp '$input_maf' uncompressed_input.maf &&
+            ln -s '$input_maf' uncompressed_input.maf &&
         #end if
         maf2hal
             #if $refGenome: