Mercurial > repos > sanbi-uwc > novo_sort
changeset 3:9c51aca51902 draft
planemo upload for repository https://github.com/zipho/novo_sort commit c490d694fa0be39bcd5048981cf4f08cd0821a50
| author | sanbi-uwc |
|---|---|
| date | Fri, 01 Apr 2016 09:53:18 -0400 |
| parents | a796191ac77a |
| children | 146641fe5ff6 |
| files | novo_sort.py novo_sort.xml |
| diffstat | 2 files changed, 2 insertions(+), 1 deletions(-) [+] |
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--- a/novo_sort.py Thu Mar 31 09:58:51 2016 -0400 +++ b/novo_sort.py Fri Apr 01 09:53:18 2016 -0400 @@ -24,6 +24,7 @@ def main(): parser = argparse.ArgumentParser(description="Re-sorting aligned files by read position") + parser.add_argument('output_filename') parser.add_argument('--bam_filename') args = parser.parse_args()
--- a/novo_sort.xml Thu Mar 31 09:58:51 2016 -0400 +++ b/novo_sort.xml Fri Apr 01 09:53:18 2016 -0400 @@ -10,7 +10,7 @@ <exit_code range="1:" /> </stdio> <command interpreter="python"> - novo_sort.py --bam_filename ${input1} + novo_sort.py '${out_file}' --bam_filename ${input1} </command> <inputs> <param name="input1" type="data" format="bam" label="Select first set of reads" help="Specify dataset with forward reads"/>