From 99000fbed3b6c13274a3ddf9eb58310cb40653f7 Mon Sep 17 00:00:00 2001 From: Jelle Scholtalbers Date: Fri, 18 Nov 2016 14:49:32 +0100 Subject: [PATCH] update rename dataset action to accept . in repeat input parameters, also when not using additional operations like '|basename'. e.g. for filter bam 0.0.1: #{input_bams_0.input_bam} and #{input_bams_0.input_bam|basename} work. And for filter bam 0.0.2: #{input_bams1} and #{input_bams2|basename} work. --- lib/galaxy/jobs/actions/post.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/lib/galaxy/jobs/actions/post.py b/lib/galaxy/jobs/actions/post.py index 834fc9c6c42..674bd5ff9b3 100644 --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -124,13 +124,16 @@ class RenameDatasetAction(DefaultJobAction): if len(tokens) > 1: input_file_var = tokens[0].strip() - # Treat . as special symbol (breaks parameter names anyway) - # to allow access to repeat elements, for instance first - # repeat in cat1 would be something like queries_0.input2. - input_file_var = input_file_var.replace(".", "|") - for i in range(1, len(tokens)): operations.append(tokens[i].strip()) + + # Treat . as special symbol (breaks parameter names anyway) + # to allow access to repeat elements, for instance first + # repeat in cat1 would be something like queries_0.input2. + # TODO: update the help text (input_terminals) on the action to + # show correct valid inputs. + input_file_var = input_file_var.replace(".", "|") + replacement = "" # Lookp through inputs find one with "to_be_replaced" input # variable name, and get the replacement name