# HG changeset patch # User sanbi-uwc # Date 1480429090 18000 # Node ID bfe39c503a40db14920033db1f93e65b56ca276c # Parent dbeac2baa4dc8b4793c9dac50939287a51ead904 planemo upload for repository https://github.com/zipho/novo_align commit 896a5a73f2a5f71a7b38dc0403f54afba1f27643 diff -r dbeac2baa4dc -r bfe39c503a40 novo_align.py --- a/novo_align.py Thu Apr 07 09:55:31 2016 -0400 +++ b/novo_align.py Tue Nov 29 09:18:10 2016 -0500 @@ -3,9 +3,11 @@ import argparse import shlex import os +import sys import logging log = logging.getLogger( __name__ ) + def novo_align(output_filename, index_filename, fwd_file, rev_file ): param = r'@RG\tID:RG\tSM:$i\tPL:ILLUMINA' cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' | samtools view -bS - > {}".format( @@ -19,6 +21,7 @@ except: print("Error running the nova-align", file=sys.stderr) + def newSplit(value): lex = shlex.shlex(value) lex.quotes = '"' @@ -26,6 +29,7 @@ lex.commenters = '' return list(lex) + def main(): parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool") parser.add_argument('output_filename') @@ -33,9 +37,10 @@ parser.add_argument('--forward_filename') parser.add_argument('--reverse_filename') args = parser.parse_args() - + # a dirty way of referencing the file index_file_path = args.index_filename + "/" + args.index_filename.split("/")[-1] novo_align(args.output_filename, index_file_path, args.forward_filename, args.reverse_filename) -if __name__ == "__main__": main() +if __name__ == "__main__": + main() diff -r dbeac2baa4dc -r bfe39c503a40 novo_align.xml --- a/novo_align.xml Thu Apr 07 09:55:31 2016 -0400 +++ b/novo_align.xml Tue Nov 29 09:18:10 2016 -0500 @@ -9,16 +9,95 @@ - - novo_align.py '${out_file}' --index_file ${index1.fields.path} --forward_file ${fastq_input1} --reverse_file ${fastq_input2} - + + + + + + + + + + + + + + + + + + + + + + + + + + +