comparison read2mut.xml @ 16:30aec05d04d3 draft

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

15:6f4c61123a36

        $chimera_correction
        --outputFile '$output_xlsx'
        --outputFile_csv '$outputFile_csv'
        --outputFile2 '$output_xlsx2'
        --outputFile3 '$output_xlsx3'
    ]]>
    </command>
    <inputs>
        <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See Help section below for a detailed explanation."/>
        <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."/>

        <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."/>
        <param name="delim_csv" type="string" 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 ${on_string}: XLSX summary"/>
        <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/>
        <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/>

16:30aec05d04d3

        $chimera_correction
        --outputFile '$output_xlsx'
        --outputFile_csv '$outputFile_csv'
        --outputFile2 '$output_xlsx2'
        --outputFile3 '$output_xlsx3'
        --delim_csv '$delim_csv'
    ]]>
    </command>
    <inputs>
        <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See Help section below for a detailed explanation."/>
        <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."/>

        <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."/>
        <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 ${on_string}: XLSX summary"/>
        <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/>
        <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/>