Mercurial > repos > sanbi-uwc > summarize_poliovirus_alignment
changeset 5:7bcfc97b9284 draft default tip
planemo upload for repository https://github.com/pvanheus/polio_report commit 753aad311378b064f2152c8e99e7c8097c7f4321-dirty
| author | sanbi-uwc |
|---|---|
| date | Fri, 11 Nov 2022 06:19:00 +0000 |
| parents | eae57366bc55 |
| children | |
| files | summarize_alignment.py summarize_poliovirus_alignment.xml |
| diffstat | 2 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/summarize_alignment.py Fri Jul 22 10:01:30 2022 +0000 +++ b/summarize_alignment.py Fri Nov 11 06:19:00 2022 +0000 @@ -30,6 +30,7 @@ alignment_summary["mismatches"], alignment_summary["perc_mismatches"], round(alignment_summary["quality"], 2), + alignment_summary["vp1_coverage_perc"], mismatch_list, sep="\t", file=summary_output,
--- a/summarize_poliovirus_alignment.xml Fri Jul 22 10:01:30 2022 +0000 +++ b/summarize_poliovirus_alignment.xml Fri Nov 11 06:19:00 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="summarize_poliovirus_alignment" name="Summarize poliovirus alignment" version="0.2.0+galaxy1" profile="21.05"> +<tool id="summarize_poliovirus_alignment" name="Summarize poliovirus alignment" version="0.3.0+galaxy1" profile="21.05"> <requirements> <requirement type="package" version="3.9">python</requirement> </requirements> @@ -22,7 +22,7 @@ <outputs> <data name="output1" format="tabular" label="Poliovirus variant summary on ${on_string}"> <actions> - <action name="column_names" type="metadata" default="sample name,best matching reference,num variants,perc variants,quality,variant list" /> + <action name="column_names" type="metadata" default="sample name,best matching reference,num variants,perc variants,quality,vp1 coverage,variant list" /> </actions> </data> <collection name="variant_list" type="list" label="Poliovirus variant lists on ${on_string}" structured_like="alignment_assessments" format="tabular">