Mercurial > repos > sanbi-uwc > novo_sort
changeset 7:2f3d4c867e1d draft default tip
planemo upload for repository https://github.com/zipho/novo_sort commit 4db125fcd73327813d7bd511852bbe9ffc68a25c
| author | sanbi-uwc |
|---|---|
| date | Mon, 09 Jan 2017 08:19:31 -0500 |
| parents | e35fbd921b6b |
| children | |
| files | novo_sort.py novo_sort.xml test-data/input1.bam test-data/output1.bam |
| diffstat | 4 files changed, 20 insertions(+), 12 deletions(-) [+] |
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--- a/novo_sort.py Fri Apr 01 10:26:19 2016 -0400 +++ b/novo_sort.py Mon Jan 09 08:19:31 2017 -0500 @@ -7,6 +7,7 @@ import logging log = logging.getLogger( __name__ ) + def novo_sort( bam_filename, output_filename ): cmdline_str = "novosort -c 8 -m 8G -s -f {} -o {}".format( bam_filename, output_filename ) cmdline = newSplit(cmdline_str) @@ -15,6 +16,7 @@ except CalledProcessError: print("Error running the nova-sort", file=sys.stderr) + def newSplit(value): lex = shlex.shlex(value) lex.quotes = '"' @@ -22,12 +24,15 @@ lex.commenters = '' return list(lex) + 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() - + novo_sort(args.bam_filename, args.output_filename) -if __name__ == "__main__": main() + +if __name__ == "__main__": + main()
--- a/novo_sort.xml Fri Apr 01 10:26:19 2016 -0400 +++ b/novo_sort.xml Mon Jan 09 08:19:31 2017 -0500 @@ -1,29 +1,32 @@ <?xml version="1.0" encoding="utf-8" ?> -<tool id="novo_sort" name="NOVO SORT" version="0.0.1"> +<tool id="novo_sort" name="NOVO SORT" version="0.0.2"> <description>Tool to run the Novo Sort mapping tool</description> <requirements> <requirement type="package" version="1.2">samtools</requirement> - <requirement type="package" version="3.04.01">novocraft</requirement> + <requirement type="package" version="3.04.04">novoalign</requirement> </requirements> - <stdio> - <exit_code range=":-1" /> - <exit_code range="1:" /> - </stdio> - <command interpreter="python"> - novo_sort.py '${out_file}' --bam_filename ${input1} + <command detect_errors="aggressive"><![CDATA[ + python $__tool_directory__/novo_sort.py '${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"/> + <param name="input1" type="data" format="bam" label="BAM file" help="a BAM file that requires sorting"/> </inputs> <outputs> <data format="bam" name="out_file" /> </outputs> - <help>Help!</help> + <help><![CDATA[ + Novosort is part of the `Novoalign`_ tool suite. + + .. _Novoalign: http://www.novocraft.com/products/novoalign/ + ]]></help> <citations> <citation></citation> </citations> <tests> <test> + <param name="input1" value="input1.bam" ftype="bam" /> + <param name="out_file" value="output1.bam" ftype="bam" /> </test> </tests> </tool>