Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.xml @ 2:9d74f30275c6 draft

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planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Wed, 07 Oct 2020 10:57:15 +0000
parents 2a505d46f682
children 4fc62ab6e9e8
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1:2a505d46f682 2:9d74f30275c6
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="read2mut" name="Call specific mutations in reads:" version="1.0.2" profile="17.01"> 2 <tool id="read2mut" name="Call specific mutations in reads:" version="1.0.3" profile="19.01">
3 <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description> 3 <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
4 <macros> 4 <macros>
5 <import>va_macros.xml</import> 5 <import>va_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"> 7 <expand macro="requirements">
28 <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"/> 28 <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"/>
29 <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."/> 29 <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."/>
30 <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."/> 30 <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."/>
31 <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."/> 31 <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."/>
32 <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."/> 32 <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."/>
33 <param name="chimera_correction" type="boolean" label="Apply chimera correction?" truevalue="--chimera_correction" falsevalue="" checked="False" help="Add additional tier for chimeric variants and correct the variant frequencies."/> 33 <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."/>
34 </inputs> 34 </inputs>
35 <outputs> 35 <outputs>
36 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX"/> 36 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX"/>
37 </outputs> 37 </outputs>
38 <tests> 38 <tests>