Mercurial > repos > jowong > add_sample_as_first_line
changeset 2:c60511d9c6be draft default tip
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit f3fe76f6cbf17b0ec4162065206483652a6519b7-dirty
| author | jowong |
|---|---|
| date | Fri, 09 Nov 2018 12:13:19 -0500 |
| parents | 45be17ffad90 |
| children | |
| files | add_sample_name_as_first_line.py add_sample_name_as_first_line.xml |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/add_sample_name_as_first_line.py Sun Oct 21 09:36:07 2018 -0400 +++ b/add_sample_name_as_first_line.py Fri Nov 09 12:13:19 2018 -0500 @@ -6,7 +6,7 @@ the_parser = argparse.ArgumentParser(description="add label to first line of file") the_parser.add_argument('--input', required=True, action="store", type=str, help="input file") the_parser.add_argument('--output', required=True, action="store", type=str, help="output file path") - the_parser.add_argument('--label', required=True, action="store", type=str, help="label to add in the first line") + the_parser.add_argument('--sample', required=True, action="store", type=str, help="label to add in the first line") args = the_parser.parse_args() return args @@ -17,7 +17,7 @@ #print >> output, args.label #print >> output, input -sample_name = re.sub('(_1.fastq.gz|_2.fastq.gz|.fastq.gz)', '', args.label.rstrip().lstrip()) +sample_name = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', args.sample.rstrip().lstrip()) with open(args.input) as input: with open(args.output, 'w') as output:
--- a/add_sample_name_as_first_line.xml Sun Oct 21 09:36:07 2018 -0400 +++ b/add_sample_name_as_first_line.xml Fri Nov 09 12:13:19 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="my_addName" name="Add sample name as first line" version="0.1.0"> +<tool id="my_addName" name="Add sample name as first line" version="0.1.2"> <description>to an existing tabular file</description> <command interpreter="python">add_sample_name_as_first_line.py --input "$input" @@ -23,7 +23,7 @@ <help> **What it does** -Adds a new line with the name of the sample file and removing [_12].fastq.gz from the name if there is match to the pattern. +Adds a new line with the name of the sample file and removing [(_1|_2)]*.fastq(.gz)* from the name if there is match to the pattern. Written by Johnathan Kwan Long Wong, johnathanwong4@gmail.com </help> <citations>