view qualimap_bamqc.xml @ 7:7923e67fa16a draft default tip

planemo upload for repository https://github.com/zipho/qualimap2 commit cdfee65aff3863f6477339300a4a11657d7a44c0

<?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
            --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="text" value="8G" format="txt" label="Java memory size (default Gig)" help="Specify the size of memory to allocate. (Default 8 Gig)"/>
    </inputs>
    <outputs>
        <data format="genomecov" name="genomecov_file" label="QualiMap: BamQC GenomeCov output"/>
    </outputs>
    <help>Help!</help>
    <citations>
        <citation></citation>
    </citations>
    <tests>
        <test>
        </test>
    </tests>
</tool>