# HG changeset patch # User simon-gladman # Date 1405015574 14400 # Node ID 70953ccd575ad591137222c280b07d671b24b907 # Parent f6cf403633965a61b98960075290be2809a438d6 Uploaded diff -r f6cf40363396 -r 70953ccd575a trimmomatic.xml --- a/trimmomatic.xml Thu Jul 10 13:38:23 2014 -0400 +++ b/trimmomatic.xml Thu Jul 10 14:06:14 2014 -0400 @@ -8,17 +8,10 @@ trimmomatic_wrapper.pl paired ${paired.is_paired} - #if $paired.is_paired == "single": - fwdfile ${paired.forwards_file} - #end if - #if $paired.is_paired == "paired": - fwdfile ${paired.forwards_file} + fwdfile ${paired.forwards_file} + #if $paired.is_paired: revfile ${paired.reverse_file} #end if - #if $paired.is_paired == "collection": - fwdfile ${collection_data.forward} - revfile ${collection_data.reverse} - #end if phred $phred cutadapt ${adapt.adapters} #if $adapt.adapters: @@ -66,12 +59,7 @@ - - - - - - + @@ -79,9 +67,6 @@ - - - @@ -154,13 +139,13 @@ - - (paired['is_paired']=="single") + + (paired['is_paired']) - - (paired['is_paired'] == "paired" or paired['is_paired'] == "collection") + + (paired['is_paired']) - +