comparison clipping_profile.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_clipping_profile" name="Clipping Profile" version="2.4galaxy1">
    <description>
     estimates clipping profile of RNA-seq reads from BAM or SAM file
    </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[clipping_profile.py --version]]></version_command>

    <command><![CDATA[
        clipping_profile.py -i $input -o output
        ]]>
    </command>

    <inputs>
        <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
    </inputs>

    <outputs>
        <data format="pdf" name="outputpdf" from_work_dir="output.clipping_profile.pdf" />
        <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" />
        <data format="txt" name="outputr" from_work_dir="output.clipping_profile.r" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <output name="outputpdf" file="output.clipping_profile.pdf"/>
            <output name="outputxls" file="output.clipping_profile.xls"/>
            <output name="outputr" file="output.clipping_profile.r"/>
        </test>
    </tests>

    <help><![CDATA[
clipping_profile.py

Inputs
++++++++++++++

Input BAM/SAM file
	Alignment file in BAM/SAM format.


Sample Output
++++++++++++++

.. image:: http://rseqc.sourceforge.net/_images/clipping_good.png
   :height: 600 px
   :width: 600 px
   :scale: 80 %

-----

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_clipping_profile" name="Clipping Profile" version="@WRAPPER_VERSION@">
    <description>
     estimates clipping profile of RNA-seq reads from BAM or SAM file
    </description>

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

    <expand macro="requirements" />

    <expand macro="stdio" />

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

    <command><![CDATA[
        clipping_profile.py -i '${input}' -o output -q ${mapq} -s "${layout}"
        ]]>
    </command>

    <inputs>
        <expand macro="bam_param" />
        <expand macro="mapq_param" />
        <expand macro="layout_param" />
        <expand macro="rscript_output_param" />
    </inputs>

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

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
            <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" />
            <output name="outputxls" file="output.clipping_profile.xls" />
        </test>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
            <param name="rscript_output" value="true" />
            <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" />
            <output name="outputxls" file="output.clipping_profile.xls" />
            <output name="outputr" file="output.clipping_profile.r" />
        </test>
    </tests>

    <help><![CDATA[
clipping_profile.py

Inputs
++++++++++++++

Input BAM/SAM file
    Alignment file in BAM/SAM format.

Minimum mapping quality
    Minimum mapping quality for an alignment to be considered as "uniquely
    mapped". default=30

Sequencing layout
    Denotes whether the sequecing was single-end (SE) or paired-end (PE).

Sample Output
++++++++++++++

.. image:: $PATH_TO_IMAGES/clipping_good.png
   :height: 600 px
   :width: 600 px
   :scale: 80 %

@ABOUT@

]]>
    </help>

    <expand macro="citations" />