Mercurial > repos > sanbi-uwc > summarize_poliovirus_alignment
changeset 2:5c8dfc4d9d68 draft
planemo upload for repository https://github.com/pvanheus/polio_report commit a99e10fec2fac5aae70974c977eb3b362a1a8429-dirty
author | sanbi-uwc |
---|---|
date | Thu, 21 Jul 2022 16:43:55 +0000 |
parents | f2a7aaf93a1d |
children | 09b98e40ab59 |
files | summarize_alignment.py summarize_poliovirus_alignment.xml |
diffstat | 2 files changed, 3 insertions(+), 1 deletions(-) [+] |
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--- a/summarize_alignment.py Tue Jul 19 11:57:59 2022 +0000 +++ b/summarize_alignment.py Thu Jul 21 16:43:55 2022 +0000 @@ -14,6 +14,7 @@ parser.add_argument("--datasets", nargs="+") args = parser.parse_args() + galaxy_metadata = {} summary_output = open(args.summary_output_filename, "w") for i, json_filename in enumerate(args.datasets): alignment_summary = json.load(open(json_filename)) @@ -27,6 +28,7 @@ alignment_summary["sample_name"], alignment_summary["best_reference"], alignment_summary["mismatches"], + alignment_summary["perc_mismatches"], round(alignment_summary["quality"], 2), mismatch_list, sep="\t",
--- a/summarize_poliovirus_alignment.xml Tue Jul 19 11:57:59 2022 +0000 +++ b/summarize_poliovirus_alignment.xml Thu Jul 21 16:43:55 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="summarize_poliovirus_alignment" name="Summarize poliovirus alignment" version="0.1.0+galaxy1" profile="21.05"> +<tool id="summarize_poliovirus_alignment" name="Summarize poliovirus alignment" version="0.2.0+galaxy0" profile="21.05"> <requirements> <requirement type="package" version="3.9">python</requirement> </requirements>