comparison read_quality.xml @ 51:09846d5169fa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83

50:f242ee103277

<tool id="rseqc_read_quality" name="Read Quality" version="2.4galaxy1">
    <description>determines Phred quality score</description>

    <macros>
        <import>rseqc_macros.xml</import>
    </macros>

    <requirements>
        <expand macro="requirement_package_r" />
        <expand macro="requirement_package_numpy" />
        <expand macro="requirement_package_rseqc" />
    </requirements>

    <expand macro="stdio" />

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

    <command><![CDATA[
        read_quality.py
            --input-file $input
            --out-prefix output
            -r $reduce
            --mapq $mapq
        ]]>
    </command>

    <inputs>
        <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
        <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/>
        <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" />
    </inputs>

    <outputs>
        <data format="txt" name="outputr" from_work_dir="output.qual.r" label="${tool.name} on ${on_string} (R Script)" />
        <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap PDF)" />
        <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot PDF)" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
            <output name="outputr" file="output.qual.r"/>
        </test>
    </tests>

    <help><![CDATA[
read_quality.py

Output
++++++++++++++

1. output.qual.r
2. output.qual.boxplot.pdf
    .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.plot.png
        :height: 600 px
        :width: 600 px
        :scale: 80 %
3. output.qual.heatmap.pdf
    .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.heatmap.png
        :height: 600 px
        :width: 600 px
        :scale: 80 %

Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density")

-----

About RSeQC
+++++++++++

The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.

The RSeQC package is licensed under the GNU GPL v3 license.

.. image:: http://rseqc.sourceforge.net/_static/logo.png

.. _RSeQC: http://rseqc.sourceforge.net/
]]>
    </help>

    <expand macro="citations" />

51:09846d5169fa

<tool id="rseqc_read_quality" name="Read Quality" version="@WRAPPER_VERSION@">
    <description>determines Phred quality score</description>

    <macros>
        <import>rseqc_macros.xml</import>
    </macros>

    <expand macro="requirements" />

    <expand macro="stdio" />

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

    <command><![CDATA[
        read_quality.py
            --input-file '${input}'
            --out-prefix output
            -r ${reduce}
            --mapq ${mapq}
        ]]>
    </command>

    <inputs>
        <expand macro="bam_sam_param" />
        <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/>
        <expand macro="mapq_param" />
        <expand macro="rscript_output_param" />
    </inputs>

    <outputs>
        <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap pdf)" />
        <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot pdf)" />
        <expand macro="rscript_output_data" filename="output.qual.r" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
            <param name="rscript_output" value="true" />
            <output name="outputr" file="output.qual.r"/>
            <output name="outputheatpdf" file="output.qual.heatmap.pdf" compare="sim_size" />
            <output name="outputboxpdf" file="output.qual.boxplot.pdf" compare="sim_size" />
        </test>
    </tests>

    <help><![CDATA[
read_quality.py

Output
++++++++++++++

1. output.qual.r
2. output.qual.boxplot.pdf
    .. image:: $PATH_TO_IMAGES/36mer.qual.plot.png
        :height: 600 px
        :width: 600 px
        :scale: 80 %
3. output.qual.heatmap.pdf
    .. image:: $PATH_TO_IMAGES/36mer.qual.heatmap.png
        :height: 600 px
        :width: 600 px
        :scale: 80 %

Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density")

@ABOUT@

]]>
    </help>

    <expand macro="citations" />