--- a/read2mut.xml	Mon Feb 22 16:56:05 2021 +0000
+++ b/read2mut.xml	Wed Feb 24 09:39:24 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="read2mut" name="Call specific mutations in reads:" version="2.0.1" profile="19.01">
+<tool id="read2mut" name="Call specific mutations in reads:" version="2.0.4" profile="17.01">
     <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
     <macros>
         <import>va_macros.xml</import>
@@ -17,9 +17,11 @@
         --sscsJson '$file4'
         --thresh '$thresh'
         --phred '$phred'
-        --trim '$trim'
+        --trim5 '$trim5'
+        --trim3 '$trim3'
         $chimera_correction
         --outputFile '$output_xlsx'
+        --outputFile_csv '$outputFile_csv'
         --outputFile2 '$output_xlsx2'
         --outputFile3 '$output_xlsx3'
     ]]>
@@ -31,11 +33,13 @@
         <param name="file4" type="data" format="json" label="JSON File with SSCS tag stats" optional="false" help="JSON file generated by DCS mutations to SSCS stats."/>
         <param name="thresh" type="integer" label="Tag count threshold" value="0" help="Integer threshold for displaying mutations. Only mutations occuring in DCS of less than thresh tags are displayed. Default of 0 displays all."/>
         <param name="phred" type="integer" label="Phred quality score threshold" min="0" max="41" value="20" help="Integer threshold for Phred quality score. Only reads higher than this threshold are considered. Default = 20."/>
-        <param name="trim" type="integer" label="Trimming threshold" value="10" help="Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10."/>
+        <param name="trim5" type="integer" label="Trimming threshold at 5' end" value="10" help="Integer threshold for assigning mutations at the beginning of reads to lower tier. Default 10."/>
+        <param name="trim3" type="integer" label="Trimming threshold at 3' end" value="10" help="Integer threshold for assigning mutations at the end of reads to lower tier. Default 10."/>
         <param name="chimera_correction" type="boolean" label="Apply chimera correction?" truevalue="--chimera_correction" falsevalue="" checked="False" help="Count chimeric variants and correct the variant frequencies."/>
     </inputs>
     <outputs>
         <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>
+        <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/>
         <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/>
         <data name="output_xlsx3" format="xlsx" label="${tool.name} on ${on_string}: XLSX tiers"/>
     </outputs>
@@ -47,9 +51,11 @@
             <param name="file4" value="SSCS_counts_test.json"/>
             <param name="thresh" value="0"/>
             <param name="phred" value="20"/>
-            <param name="trim" value="10"/>
-            <param name="chimera_correction" value="True"/>
+            <param name="trim5" value="10"/>
+            <param name="trim3" value="10"/>
+            <param name="delim_csv" value=","/>
             <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"/>
             <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/>
         </test>