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update rename dataset action to accept . in repeat input parameters, also when not using additional operations like '|basename'.

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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.
This commit is contained in:
Jelle Scholtalbers
2016-11-18 14:49:39 +01:00
parent 33894ca744
commit 99000fbed3
1 changed files with 8 additions and 5 deletions
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lib/galaxy/jobs/actions/post.py
+8 -5
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@@ -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