diff read2mut.xml @ 55:8fbe6aba07e5 draft

planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

--- a/read2mut.xml	Fri Mar 12 08:00:31 2021 +0000
+++ b/read2mut.xml	Fri Mar 12 14:18:45 2021 +0000
@@ -1,5 +1,5 @@
 <?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="2.1.1" profile="19.01">
     <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
     <macros>
         <import>va_macros.xml</import>
@@ -26,6 +26,7 @@
         --softclipping_dist '$softclipping_dist'
         --reads_threshold '$reads_threshold'
         --outputFile '$output_xlsx'
+        --outputFile_csv '$outputFile_csv'
         --outputFile2 '$output_xlsx2'
         --outputFile3 '$output_xlsx3'
     ]]>
@@ -44,6 +45,7 @@
     </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>
@@ -60,6 +62,7 @@
             <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="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>
@@ -75,7 +78,7 @@
 **Input** 
 
 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. 
-generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_.
+generated by the `FreeBayes <https://arxiv.org/abs/1207.3907>`_ or `LoFreq <https://academic.oup.com/nar/article/40/22/11189/1152727>`_ variant caller.
 
 **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>`_.
@@ -91,9 +94,10 @@
 **Output**
 
 The output are three XLSX files containing frequencies stats for DCS mutations based 
-on information from the raw reads. In addition to that a tier based 
+on information from the raw reads and a CSV file containing the summary information without color-coding. In addition to that a tier based 
 classification is provided based on the amout of support for a true variant call.
 
+
     ]]> 
     </help>
     <expand macro="citation" />