comparison read_duplication.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>determines reads duplication rate with sequence-based and mapping-based strategies</description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>

    <expand macro="requirements" />

    <expand macro="stdio" />

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

    <command><![CDATA[
        @BAM_SAM_INPUTS@
        read_duplication.py -i 'input.${extension}' -o output -u ${upLimit} -q ${mapq}
        ]]>
    </command>

    <inputs>
        <expand macro="bam_sam_param" />
        <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" help="(--up-limit)"/>
        <expand macro="mapq_param" />
        <expand macro="rscript_output_param" />
    </inputs>

    <outputs>
        <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf"  label="${tool.name} on ${on_string}: plot (PDF)"/>
        <data format="tabular" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string}: positon"/>
        <data format="tabular" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string}: sequences"/>
        <expand macro="rscript_output_data" filename="output.DupRate_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
    </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.pos.DupRate.xls" ftype="tabular"/>
            <output name="outputseqxls" file="output.seq.DupRate.xls" ftype="tabular"/>
            <output name="outputr" file="output.DupRate_plot_r" />
            <output name="outputpdf" file="output.DupRate_plot.pdf" compare="sim_size" />
        </test>
    </tests>

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

Two strategies were used to determine reads duplication rate:

@ABOUT@

]]>
    </help>

    <expand macro="citations" />

</tool>

63:27e16a30667a

    <description>determines reads duplication rate with sequence-based and mapping-based strategies</description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <version_command><![CDATA[read_duplication.py --version]]></version_command>
    <command><![CDATA[
        @BAM_SAM_INPUTS@
        read_duplication.py -i 'input.${extension}' -o output -u ${upLimit} -q ${mapq}
        ]]>
    </command>
    <inputs>
        <expand macro="bam_sam_param" />
        <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" help="(--up-limit)"/>
        <expand macro="mapq_param" />
        <expand macro="rscript_output_param" />
    </inputs>
    <outputs>
        <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf"  label="${tool.name} on ${on_string}: plot (PDF)"/>
        <data format="tabular" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string}: positon"/>
        <data format="tabular" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string}: sequences"/>
        <expand macro="rscript_output_data" filename="output.DupRate_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
    </outputs>
    <tests>
        <test expect_num_outputs="4">
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
            <param name="rscript_output" value="true" />
            <output name="outputxls" file="output.pos.DupRate.xls" ftype="tabular"/>
            <output name="outputseqxls" file="output.seq.DupRate.xls" ftype="tabular"/>
            <output name="outputr" file="output.DupRate_plot_r" />
            <output name="outputpdf" file="output.DupRate_plot.pdf" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
read_duplication.py
+++++++++++++++++++

Two strategies were used to determine reads duplication rate:

@ABOUT@

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