comparison read2mut.xml @ 2:9d74f30275c6 draft

planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

1:2a505d46f682

<?xml version="1.0" encoding="UTF-8"?>
<tool id="read2mut" name="Call specific mutations in reads:" version="1.0.2" profile="17.01">
    <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
    <macros>
        <import>va_macros.xml</import>
    </macros>
    <expand macro="requirements">

        <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="Add additional tier for chimeric variants and correct the variant frequencies."/>
    </inputs>
    <outputs>
        <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX"/>
    </outputs>
    <tests>

2:9d74f30275c6

<?xml version="1.0" encoding="UTF-8"?>
<tool id="read2mut" name="Call specific mutations in reads:" version="1.0.3" profile="19.01">
    <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
    <macros>
        <import>va_macros.xml</import>
    </macros>
    <expand macro="requirements">

        <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>