# HG changeset patch
# User sanbi-uwc
# Date 1668147540 0
# Node ID 7bcfc97b92841c36e201a48e69782789582c8d18
# Parent  eae57366bc55fca96d18d1877dd1cadc2ae89da4
planemo upload for repository https://github.com/pvanheus/polio_report commit 753aad311378b064f2152c8e99e7c8097c7f4321-dirty

diff -r eae57366bc55 -r 7bcfc97b9284 summarize_alignment.py
--- 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,
diff -r eae57366bc55 -r 7bcfc97b9284 summarize_poliovirus_alignment.xml
--- 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">