view qualimap_bamqc.xml @ 0:d87d6c0c27f5 draft

planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0

<?xml version="1.0" encoding="utf-8" ?>
<tool id="qualimap_bamqc" name="QualiMap BamQC" version="2.2">
    <description>Tool to to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.</description>
    <requirements>
        <requirement type="package" version="2.2">qualimap</requirement>
    </requirements>
    <stdio>
        <exit_code range=":-1" />
        <exit_code range="1:" />
    </stdio>
    <command interpreter="python">
        qualimap_bamqc.py
            --input_file ${input_realigned_bam_file}
            --out_genome_file ${genomecov_file}
            --out_dir ${genomecov_file.files_path}
            --out_pdf_file ${pdf_file}
            --java-mem-size ${mem_size}
    </command>
    <inputs>
        <param name="input_realigned_bam_file" type="data" format="bam" label="Realigned BAM dataset" help="Specify realigned BAM dataset"/>
        <param name="mem_size" type="txt" format="txt" label="Java memory size (default Gig)" help="Specify the size of memory to allocate to the Job with default 8 Gig"/>
    </inputs>
    <outputs>
        <data format="genomecov" name="genomecov_file" label="QualiMap: BamQC GenomeCov output"/>
        <data format="pdf" name="pdf_file" label="QualiMap: BamQC PDF output"/>
    </outputs>
    <help>Help!</help>
    <citations>
        <citation></citation>
    </citations>
    <tests>
        <test>
        </test>
    </tests>
</tool>