Mercurial > repos > sanbi-uwc > summarize_poliovirus_alignment

changeset 2:5c8dfc4d9d68 draft

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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(-) [+]
line wrap: on
line diff
--- 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>