# HG changeset patch # User greg # Date 1452454547 18000 # Node ID 67171d711b345d5f1c59c2eac63cc83aa57046d3 # Parent b740d423ce0749730fe6cca3e5d2e7bc13065bf1 Uploaded diff -r b740d423ce07 -r 67171d711b34 fasta_extract.xml --- a/fasta_extract.xml Sun Jan 10 14:25:59 2016 -0500 +++ b/fasta_extract.xml Sun Jan 10 14:35:47 2016 -0500 @@ -13,11 +13,11 @@ --input "$i" ${i.hid} #end for #if str($reference_genome_cond.reference_genome_source) == "cached": - #set genome_file = "$reference_genome_cond.reference_genome.fields.path" + #set genome_file = $reference_genome_cond.reference_genome.fields.path #else: - #set genome_file = "$reference_genome_cond.reference_genome" + #set genome_file = $reference_genome_cond.reference_genome #end if - --genome_file $genome_file + --genome_file "$genome_file" --subtract_from_start $subtract_from_start --add_to_end $add_to_end --extend_existing $extend_existing