Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.xml @ 24:cf6f0fb05bad 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 16:31:04 +0000
parents 858ca8b7ad43
children 5992e30ae50e
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23:25625221b88f 24:cf6f0fb05bad
31 <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."/> 31 <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."/>
32 <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"/> 32 <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"/>
33 <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."/> 33 <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."/>
34 <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."/> 34 <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."/>
35 <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."/> 35 <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."/>
36 <param name="trim5" type="integer" label="Trimming threshold at 5' end" value="10" help="Integer threshold for assigning mutations at start of reads to lower tier. Default 10."/> 36 <param name="trim5" type="integer" label="Trimming threshold at 5' end" value="10" help="Integer threshold for assigning mutations at the beginning of reads to lower tier. Default 10."/>
37 <param name="trim3" type="integer" label="Trimming threshold at 3' end" value="10" help="Integer threshold for assigning mutations at end of reads to lower tier. Default 10."/> 37 <param name="trim3" type="integer" label="Trimming threshold at 3' end" value="10" help="Integer threshold for assigning mutations at the end of reads to lower tier. Default 10."/>
38 <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."/> 38 <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."/>
39 </inputs> 39 </inputs>
40 <outputs> 40 <outputs>
41 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/> 41 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>
42 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/> 42 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/>