# HG changeset patch
# User public-health-bioinformatics
# Date 1572549276 14400
# Node ID 45542cd244ad3edafb5fabcd866b2ddf0795909a
# Parent 2c6153023368797e2eb5aa2bd820b71efdf3db38
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
diff -r 2c6153023368 -r 45542cd244ad screen_abricate_report.py
--- a/screen_abricate_report.py Wed Oct 30 23:01:01 2019 -0400
+++ b/screen_abricate_report.py Thu Oct 31 15:14:36 2019 -0400
@@ -30,7 +30,7 @@
gene_detection_status_fieldnames = ['gene_name', 'detected']
with open(args.abricate_report, 'r') as f1, open(args.screened_report, 'w') as f2, open(args.gene_detection_status, 'w') as f3:
abricate_report_reader = csv.DictReader(f1, delimiter="\t", quotechar='"')
- screened_report_writer = csv.DictWriter(f2, delimiter="\t", quotechar='"', fieldnames=abricate_report_fieldnames)
+ screened_report_writer = csv.DictWriter(f2, delimiter="\t", quotechar='"', fieldnames=abricate_report_reader.fieldnames)
gene_detection_status_writer = csv.DictWriter(f3, delimiter="\t", quotechar='"', fieldnames=gene_detection_status_fieldnames)
screened_report_writer.writeheader()
gene_detection_status_writer.writeheader()
diff -r 2c6153023368 -r 45542cd244ad screen_abricate_report.xml
--- a/screen_abricate_report.xml Wed Oct 30 23:01:01 2019 -0400
+++ b/screen_abricate_report.xml Thu Oct 31 15:14:36 2019 -0400
@@ -23,8 +23,10 @@
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-