# 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}
-
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