view call_amr_mutations.xml @ 3:30b17a17c1aa draft

Uploaded

<tool id="call_amr_mutations" name="PIMA: call AMR mutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
## NOTE: This tool provides the functionality of the PIMA filter_varsacn()
## function here https://github.com/appliedbinf/pima_md/blob/main/pima.py#L3012

python '$__tool_directory__/filter_varscan.py'
--varscan_raw '$varscan_raw'
--output '$output'
]]></command>
    <inputs>
        <param name="varscan_raw" type="data" format="vcf" label="Raw varscan VCF file"/>
    </inputs>
    <outputs>
        <data name="output" format="vcf"/>
    </outputs>
    <tests>
        <test>
            <param name="varscan_raw" value="input.vcf" ftype="vcf"/>
            <output name="output" value="output.vcf" ftype="vcf"/>
        </test>
    </tests>
    <help>
**What it does**

Accepts VarScan mpileup2snps VCF file, filters it, and produces a filtered VCF file.
    </help>
    <expand macro="citations"/>
</tool>