--- a/read2mut.xml	Thu Feb 04 09:01:43 2021 +0000
+++ b/read2mut.xml	Mon Feb 15 21:53:24 2021 +0000
@@ -1,16 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="read2mut" name="Call specific mutations in reads:" version="2.1.0" profile="19.01">
+<tool id="read2mut" name="Call specific mutations in reads:" version="2.0.1" profile="19.01">
     <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
     <macros>
         <import>va_macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="2.7">python</requirement>
-        <requirement type="package" version="1.4.0">matplotlib</requirement>
-        <requirement type="package" version="0.15">pysam</requirement>
+    <expand macro="requirements">
         <requirement type="package" version="1.1.0">xlsxwriter</requirement>
-        <requirement type="package" version="0.11.6">cyvcf2</requirement>
-    </requirements>
+    </expand>
     <command><![CDATA[
         ln -s '$file2' bam_input.bam &&
         ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
@@ -23,11 +19,7 @@
         --phred '$phred'
         --trim '$trim'
         $chimera_correction
-        --softclipping_dist '$softclipping_dist'
-        --reads_threshold '$reads_threshold'
         --outputFile '$output_xlsx'
-        --outputFile2 '$output_xlsx2'
-        --outputFile3 '$output_xlsx3'
     ]]>
     </command>
     <inputs>
@@ -39,13 +31,9 @@
         <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="softclipping_dist" type="integer" label="Distance between artifact and softclipping of the reads" min="1" value="15" help="Count mutation as an artifact if mutation lies within this parameter away from the softclipping part of the reads. Default = 20"/>
-<param name="reads_threshold" type="float" label="Minimum percentage of softclipped reads in a family" min="0.0" max="1.0" value="1.0" help="Float number which specifies the minimum percentage of softclipped reads in a family to be considered in the softclipping tiers. Default: 1.0, means all reads of a family have to be softclipped."/>
     </inputs>
     <outputs>
-        <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>
-        <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/>
-        <data name="output_xlsx3" format="xlsx" label="${tool.name} on ${on_string}: XLSX tiers"/>
+        <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX"/>
     </outputs>
     <tests>
         <test>
@@ -56,12 +44,8 @@
             <param name="thresh" value="0"/>
             <param name="phred" value="20"/>
             <param name="trim" value="10"/>
-            <param name="chimera_correction"/>
-            <param name="softclipping_dist" value="15"/>
-            <param name="reads_threshold" value="1.0"/>
-            <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" 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"/>
+            <param name="chimera_correction" value="True"/>
+            <output name="output_xlsx" file="Variant_Analyzer_test.xlsx" decompress="true" lines_diff="2"/>
         </test>
     </tests>
     <help> <![CDATA[
@@ -90,7 +74,7 @@
 
 **Output**
 
-The output are three XLSX files containing frequencies stats for DCS mutations based 
+The output is an XLSX file containing frequencies stats for DCS mutations based 
 on information from the raw reads. In addition to that a tier based 
 classification is provided based on the amout of support for a true variant call.