# HG changeset patch
# User mheinzl
# Date 1614011464 0
# Node ID cf6f0fb05bad254cb33f5a2eec17503360579a5a
# Parent  25625221b88f8705611192615c3f8f9f1c6066b1
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

diff -r 25625221b88f -r cf6f0fb05bad read2mut.py
--- a/read2mut.py	Mon Feb 22 16:23:48 2021 +0000
+++ b/read2mut.py	Mon Feb 22 16:31:04 2021 +0000
@@ -767,7 +767,8 @@
                     else:
                         chimeric_dcs_high_tiers += high_tiers
                 chimera_dict[key1] = (chimeric_dcs, chimeric_dcs_high_tiers)
-
+    csv_data.close()
+    
     # sheet 2
     if chimera_correction:
         header_line2 = ('variant ID', 'cvrg', 'AC alt (all tiers)', 'AF (all tiers)', 'chimeras in AC alt (all tiers)', 'chimera-corrected cvrg', 'chimera-corrected AF (all tiers)', 'cvrg (tiers 1.1-2.4)', 'AC alt (tiers 1.1-2.4)', 'AF (tiers 1.1-2.4)', 'chimeras in AC alt (tiers 1.1-2.4)', 'chimera-corrected cvrg (tiers 1.1-2.4)', 'chimera-corrected AF (tiers 1.1-2.4)', 'AC alt (orginal DCS)', 'AF (original DCS)',
@@ -973,7 +974,7 @@
     workbook.close()
     workbook2.close()
     workbook3.close()
-    csv_data.close()
+    
 
 
 if __name__ == '__main__':
diff -r 25625221b88f -r cf6f0fb05bad read2mut.xml
--- a/read2mut.xml	Mon Feb 22 16:23:48 2021 +0000
+++ b/read2mut.xml	Mon Feb 22 16:31:04 2021 +0000
@@ -33,8 +33,8 @@
         <param name="file4" type="data" format="json" label="JSON File with SSCS tag stats" optional="false" help="JSON file generated by DCS mutations to SSCS stats."/>
         <param name="thresh" type="integer" label="Tag count threshold" value="0" help="Integer threshold for displaying mutations. Only mutations occuring in DCS of less than thresh tags are displayed. Default of 0 displays all."/>
         <param name="phred" type="integer" label="Phred quality score threshold" min="0" max="41" value="20" help="Integer threshold for Phred quality score. Only reads higher than this threshold are considered. Default = 20."/>
-        <param name="trim5" type="integer" label="Trimming threshold at 5' end" value="10" help="Integer threshold for assigning mutations at start of reads to lower tier. Default 10."/>
-        <param name="trim3" type="integer" label="Trimming threshold at 3' end" value="10" help="Integer threshold for assigning mutations at end of reads to lower tier. Default 10."/>
+        <param name="trim5" type="integer" label="Trimming threshold at 5' end" value="10" help="Integer threshold for assigning mutations at the beginning of reads to lower tier. Default 10."/>
+        <param name="trim3" type="integer" label="Trimming threshold at 3' end" value="10" help="Integer threshold for assigning mutations at the end of reads to lower tier. Default 10."/>
         <param name="chimera_correction" type="boolean" label="Apply chimera correction?" truevalue="--chimera_correction" falsevalue="" checked="False" help="Count chimeric variants and correct the variant frequencies."/>
     </inputs>
     <outputs>