Mercurial > repos > mheinzl > variant_analyzer2

diff read2mut.xml @ 17:f06067bedfc5 draft

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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Mon, 22 Feb 2021 14:40:07 +0000
parents 30aec05d04d3
children 858ca8b7ad43
line wrap: on
line diff
--- 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"/>