# HG changeset patch # User iuc # Date 1539704920 14400 # Node ID d837223d4ad2df8b1801162013c14167a241393d # Parent a5a13ea16d17d5bcd7f733a98fe2717f75e8fa72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 78c3dea7dcd0c854fe7e6dc1d2b2349956167661 diff -r a5a13ea16d17 -r d837223d4ad2 picard_EstimateLibraryComplexity.xml --- a/picard_EstimateLibraryComplexity.xml Tue Jun 19 11:28:30 2018 -0400 +++ b/picard_EstimateLibraryComplexity.xml Tue Oct 16 11:48:40 2018 -0400 @@ -18,8 +18,7 @@ MAX_DIFF_RATE="${max_diff_rate}" MIN_MEAN_QUALITY="${min_mean_quality}" MAX_GROUP_RATIO="${max_group_ratio}" - #import pipes - READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" } + READ_NAME_REGEX='${ str( $read_name_regex ) }' OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" VALIDATION_STRINGENCY="${validation_stringency}" @@ -36,10 +35,7 @@ - - - - + diff -r a5a13ea16d17 -r d837223d4ad2 picard_MarkDuplicates.xml --- a/picard_MarkDuplicates.xml Tue Jun 19 11:28:30 2018 -0400 +++ b/picard_MarkDuplicates.xml Tue Oct 16 11:48:40 2018 -0400 @@ -24,9 +24,8 @@ DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}' - #import pipes #if $read_name_regex: - READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) } + READ_NAME_REGEX='${ str( $read_name_regex ) }' #end if OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}' @@ -55,11 +54,7 @@ - - - - - + diff -r a5a13ea16d17 -r d837223d4ad2 picard_MarkDuplicatesWithMateCigar.xml --- a/picard_MarkDuplicatesWithMateCigar.xml Tue Jun 19 11:28:30 2018 -0400 +++ b/picard_MarkDuplicatesWithMateCigar.xml Tue Oct 16 11:48:40 2018 -0400 @@ -26,8 +26,7 @@ DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}" - #import pipes - READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" } + READ_NAME_REGEX='${ str( $read_name_regex ) }' OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" @@ -54,10 +53,7 @@ - - - - + diff -r a5a13ea16d17 -r d837223d4ad2 picard_macros.xml --- a/picard_macros.xml Tue Jun 19 11:28:30 2018 -0400 +++ b/picard_macros.xml Tue Oct 16 11:48:40 2018 -0400 @@ -9,6 +9,17 @@ + + + + + + + + + + + 2.18.2