comparison read_NVC.xml @ 63:27e16a30667a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de

62:473382134e56

    <description>to check the nucleotide composition bias</description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>

    <expand macro="requirements" />

    <expand macro="stdio" />

    <version_command><![CDATA[read_NVC.py --version]]></version_command>

    <command><![CDATA[
        @BAM_SAM_INPUTS@
        read_NVC.py
            --input-file 'input.${extension}'
            --out-prefix output
            ${nx}
            --mapq ${mapq}
    ]]>
    </command>

    <inputs>
        <expand macro="bam_sam_param" />
        <param name="nx" type="boolean" value="false" truevalue="--nx" falsevalue="" label="Include N,X in NVC plot" help="(--nx)"/>
        <expand macro="mapq_param" />
        <expand macro="rscript_output_param" />
    </inputs>

    <outputs>
        <expand macro="pdf_output_data" filename="output.NVC_plot.pdf" />
        <expand macro="xls_output_data" filename="output.NVC.xls" />
        <expand macro="rscript_output_data" filename="output.NVC_plot.r" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
            <param name="rscript_output" value="true" />
            <output name="outputxls" file="output.NVC.xls" ftype="tabular"/>
            <output name="outputr" file="output.NVC_plot_r" />
            <output name="outputpdf" file="output.NVC_plot.pdf" compare="sim_size" />
        </test>
    </tests>

    <help><![CDATA[
read_NVC.py
+++++++++++

This module is used to check the nucleotide composition bias. Due to random priming, certain

@ABOUT@

]]>
    </help>

    <expand macro="citations" />

</tool>

63:27e16a30667a

    <description>to check the nucleotide composition bias</description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <version_command><![CDATA[read_NVC.py --version]]></version_command>
    <command><![CDATA[
        @BAM_SAM_INPUTS@
        read_NVC.py
            --input-file 'input.${extension}'
            --out-prefix output
            ${nx}
            --mapq ${mapq}
    ]]>
    </command>
    <inputs>
        <expand macro="bam_sam_param"/>
        <param name="nx" type="boolean" value="false" truevalue="--nx" falsevalue="" label="Include N,X in NVC plot" help="(--nx)"/>
        <expand macro="mapq_param"/>
        <expand macro="rscript_output_param"/>
    </inputs>
    <outputs>
        <expand macro="pdf_output_data" filename="output.NVC_plot.pdf"/>
        <expand macro="xls_output_data" filename="output.NVC.xls"/>
        <expand macro="rscript_output_data" filename="output.NVC_plot.r"/>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <param name="rscript_output" value="true"/>
            <output name="outputxls" file="output.NVC.xls" ftype="tabular"/>
            <output name="outputr" file="output.NVC_plot_r"/>
            <output name="outputpdf" file="output.NVC_plot.pdf" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
read_NVC.py
+++++++++++

This module is used to check the nucleotide composition bias. Due to random priming, certain

@ABOUT@

]]>
    </help>
    <expand macro="citations"/>
</tool>