# HG changeset patch # User yhoogstrate # Date 1424418556 18000 # Node ID dd2ec1b37e9692889dc7e3e0e56fbc83f3948f38 # Parent c6a790326d1eda4158bd6e585116631a532b60a8 Added support for the "pair"-data collection type. diff -r c6a790326d1e -r dd2ec1b37e96 sickle.xml --- a/sickle.xml Mon Jul 15 12:12:41 2013 -0500 +++ b/sickle.xml Fri Feb 20 02:49:16 2015 -0500 @@ -4,50 +4,68 @@ sickle - sickle $readtype.single_or_paired --quiet - + sickle + #if str($readtype.single_or_paired) == "se": - -f $input_single -t $qual_type -o $output_single + se + #else + pe #end if - + + --quiet + + #if str($readtype.single_or_paired) == "se": + -f $input_single -t $qual_type -o $output_single + #end if + #if str($readtype.single_or_paired) == "pe": - -f $input_paired1 -r $input_paired2 -o $output_paired1 -p $output_paired2 -s $output_paired_single -t $qual_type + -f $input_paired1 -r $input_paired2 -o $output_paired1 -p $output_paired2 -s $output_paired_single -t $qual_type #end if - + + #if str($readtype.single_or_paired) == "pe_collection": + -f "$readtype.input_paired.forward" -r "$readtype.input_paired.reverse" -o $output_paired1 -p $output_paired2 -s $output_paired_single -t $qual_type + #end if + #if str($qual_threshold) != "": - -q $qual_threshold + -q $qual_threshold #end if - + #if str($length_threshold) != "": - -l $length_threshold + -l $length_threshold #end if #if $no_five_prime: - -x + -x #end if #if $discard_n: -n #end if - + + + - + - + + + + + - + @@ -72,15 +90,15 @@ - (readtype['single_or_paired'] == 'pe') + (readtype['single_or_paired'] == 'pe' or readtype['single_or_paired'] == 'pe_collection') - (readtype['single_or_paired'] == 'pe') + (readtype['single_or_paired'] == 'pe' or readtype['single_or_paired'] == 'pe_collection') - (readtype['single_or_paired'] == 'pe') + (readtype['single_or_paired'] == 'pe' or readtype['single_or_paired'] == 'pe_collection')