comparison read2mut.xml @ 12:7a418148319d draft

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

11:84a1a3f70407

        --thresh '$thresh'
        --phred '$phred'
        --trim '$trim'
        $chimera_correction
        --outputFile '$output_xlsx'
    ]]>
    </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="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>
        <test>
            <param name="file1" value="FreeBayes_test.vcf"/>
            <param name="file2" value="Interesting_Reads_test.trim.bam"/>

            <param name="file4" value="SSCS_counts_test.json"/>
            <param name="thresh" value="0"/>
            <param name="phred" value="20"/>
            <param name="trim" value="10"/>
            <param name="chimera_correction" value="True"/>
            <output name="output_xlsx" file="Variant_Analyzer_test.xlsx" decompress="true" lines_diff="2"/>
        </test>
    </tests>
    <help> <![CDATA[
**What it does**

stats of tags that carry a mutation in the SSCS at the same position a mutation 
is called in the DCS.

**Output**

The output is an XLSX file containing frequencies stats for DCS mutations based 
on information from the raw reads. In addition to that a tier based 
classification is provided based on the amout of support for a true variant call.

    ]]> 
    </help>

12:7a418148319d

        --thresh '$thresh'
        --phred '$phred'
        --trim '$trim'
        $chimera_correction
        --outputFile '$output_xlsx'
        --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="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 ${on_string}: XLSX summary"/>
        <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/>
        <data name="output_xlsx3" format="xlsx" label="${tool.name} on ${on_string}: XLSX tiers"/>
    </outputs>
    <tests>
        <test>
            <param name="file1" value="FreeBayes_test.vcf"/>
            <param name="file2" value="Interesting_Reads_test.trim.bam"/>

            <param name="file4" value="SSCS_counts_test.json"/>
            <param name="thresh" value="0"/>
            <param name="phred" value="20"/>
            <param name="trim" value="10"/>
            <param name="chimera_correction" value="True"/>
            <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/>
            <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/>
            <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/>
        </test>
    </tests>
    <help> <![CDATA[
**What it does**

stats of tags that carry a mutation in the SSCS at the same position a mutation 
is called in the DCS.

**Output**

The output are three XLSX files containing frequencies stats for DCS mutations based 
on information from the raw reads. In addition to that a tier based 
classification is provided based on the amout of support for a true variant call.

    ]]> 
    </help>