# HG changeset patch
# User mheinzl
# Date 1614004807 0
# Node ID f06067bedfc5a0f358c07e4ad9440fc491100dd6
# Parent  30aec05d04d3f6681b41319382012614e60386a4
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

diff -r 30aec05d04d3 -r f06067bedfc5 read2mut.py
--- a/read2mut.py	Mon Feb 22 14:33:12 2021 +0000
+++ b/read2mut.py	Mon Feb 22 14:40:07 2021 +0000
@@ -63,10 +63,6 @@
                         help='Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10.')
     parser.add_argument('--chimera_correction', action="store_true",
                         help='Count chimeric variants and correct the variant frequencies')
-    parser.add_argument('--delim_csv', type=str, default=",",
-                        help='Delimiter in csv summary file. Default comma.')
-
-
     return parser
 
 
@@ -238,7 +234,7 @@
         pure_tags_dict_short = pure_tags_dict
 
     csv_data = open(outputFile_csv, "w")
-    csv_writer = csv.writer(csv_data, delimiter=delim_csv)
+    csv_writer = csv.writer(csv_data, delimiter=",")
 
     # output summary with threshold
     workbook = xlsxwriter.Workbook(outfile)
diff -r 30aec05d04d3 -r f06067bedfc5 read2mut.xml
--- a/read2mut.xml	Mon Feb 22 14:33:12 2021 +0000
+++ b/read2mut.xml	Mon Feb 22 14:40:07 2021 +0000
@@ -23,7 +23,6 @@
         --outputFile_csv '$outputFile_csv'
         --outputFile2 '$output_xlsx2'
         --outputFile3 '$output_xlsx3'
-        --delim_csv '$delim_csv'
     ]]>
     </command>
     <inputs>
@@ -35,7 +34,6 @@
         <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="trim" type="integer" label="Trimming threshold" value="10" help="Integer threshold for assigning mutations at start and 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."/>
-        <param name="delim_csv" type="text" label="Delimiter in csv file" value="," help="Delimiter in csv summary file. Default = comma."/>
     </inputs>
     <outputs>
         <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>
@@ -53,7 +51,6 @@
             <param name="phred" value="20"/>
             <param name="trim" value="10"/>
             <param name="delim_csv" value=","/>
-            <param name="chimera_correction" value="True"/>
             <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/>
             <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/>
             <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/>