diff read2mut.xml @ 2:3f1dbd2c59bf draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"

--- a/read2mut.xml	Wed Dec 04 16:21:17 2019 -0500
+++ b/read2mut.xml	Tue Nov 10 12:55:29 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="read2mut" name="Call specific mutations in reads:" version="1.0.1" profile="19.01">
+<tool id="read2mut" name="Call specific mutations in reads:" version="2.0.0" profile="19.01">
     <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
     <macros>
         <import>va_macros.xml</import>
@@ -18,45 +18,48 @@
         --thresh '$thresh'
         --phred '$phred'
         --trim '$trim'
+        $chimera_correction
         --outputFile '$output_xlsx'
     ]]>
     </command>
     <inputs>
-        <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/>
+        <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See Help section below for a detailed explanation."/>
         <param name="file2" type="data" format="bam" label="BAM File of raw reads" optional="false" help="BAM file with aligned raw reads of selected tags."/>
         <param name="file3" type="data" format="json" label="JSON File with DCS tag stats" optional="false" help="JSON file generated by DCS mutations to tags/reads"/>
         <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="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"/>
     </outputs>
     <tests>
         <test>
-            <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/>
-            <param name="file2" value="Interesting_Reads_test_data_VA.trim.bam"/>
-            <param name="file3" value="tag_count_dict_test_data_VA.json"/>
-            <param name="file4" value="SSCS_counts_test_data_VA.json"/>
+            <param name="file1" value="FreeBayes_test.vcf"/>
+            <param name="file2" value="Interesting_Reads_test.trim.bam"/>
+            <param name="file3" value="tag_count_dict_test.json"/>
+            <param name="file4" value="SSCS_counts_test.json"/>
             <param name="thresh" value="0"/>
             <param name="phred" value="20"/>
             <param name="trim" value="10"/>
-            <output name="output_xlsx" file="mutant_reads_summary_short_trim_test_data_VA.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[
 **What it does**
 
-Takes a tabular file with mutations, a BAM file of aligned raw reads, and JSON files 
+Takes a VCF file with mutations, a BAM file of aligned raw reads, and JSON files 
 created by the tools **DCS mutations to tags/reads** and **DCS mutations to SSCS stats** 
 as input and calculates frequencies and stats for DCS mutations based on information 
 from the raw reads.
 
 **Input** 
 
-**Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as 
-generated by the **Variant Annotator** tool.
+**Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. 
+generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_.
 
 **Dataset 2:** BAM file of aligned raw reads. This file can be obtained by the 
 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.