comparison RPKM_saturation.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_RPKM_saturation" name="RPKM Saturation" version="2.4galaxy1">
    <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</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[RPKM_saturation.py --version]]></version_command>

    <command><![CDATA[
        RPKM_saturation.py -i $input -o output -r $refgene

        #if str($strand_type.strand_specific) == "pair"
            -d
            #if str($strand_type.pair_type) == "sd"
                '1++,1--,2+-,2-+'

            #else
                '+-,-+'
            #end if
        #end if

        -l $percentileFloor -u $percentileCeiling -s $percentileStep -c $rpkmCutoff
        ]]>
    </command>

    <inputs>
        <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
        <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/>
        <conditional name="strand_type">
            <param name="strand_specific" type="select" label="Strand-specific?" value="None">
                <option value="none">None</option>
                <option value="pair">Pair-End RNA-seq</option>
                <option value="single">Single-End RNA-seq</option>
            </param>
            <when value="pair">
                <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd" help="(--strand)">
                    <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
                    <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
                </param>
            </when>
            <when value="single">
                <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s" help="(--strand)">
                    <option value="s">positive --> positive; negative --> negative</option>
                    <option value="d">positive --> negative; negative --> positive</option>
                </param>
            </when>
            <when value="none"></when>
        </conditional>
        <param name="percentileFloor" type="integer" value="5" label="Begin sampling from this percentile (default=5)" help="(--percentile-floor)"/>
        <param name="percentileCeiling" type="integer" value="100" label="End sampling at this percentile (default=100)" help="(--percentile-ceiling)" />
        <param name="percentileStep" type="integer" value="5" label="Sampling step size (default=5)" help="(--percentile-step)" />
        <param name="rpkmCutoff" type="text" value="0.01" label="Ignore transcripts with RPKM smaller than this number (default=0.01)" help="(--rpkm-cutoff)" />
        <param name="mapq" value="30" type="integer" label="Minimum mapping quality for an alignment to be called 'uniquly mapped'" help="(--mapq)" />
    </inputs>

    <outputs>
        <data format="xls" name="outputxls" from_work_dir="output.eRPKM.xls" label="${tool.name} on ${on_string} (RPKM XLS)"/>
        <data format="xls" name="outputrawxls" from_work_dir="output.rawCount.xls" label="${tool.name} on ${on_string} (Raw Count XLS)"/>
        <data format="txt" name="outputr" from_work_dir="output.saturation.r" label="${tool.name} on ${on_string} (R Script)"/>
        <data format="pdf" name="outputpdf" from_work_dir="output.saturation.pdf" label="${tool.name} on ${on_string} (PDF)"/>
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
            <param name="refgene" value="hg19.HouseKeepingGenes_30.bed"/>
            <output name="outputxls">
              <assert_contents>
                <has_n_columns n="26" />
                <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" />
              </assert_contents>

              <assert_contents>
                <has_text text="pdf('output.saturation.pdf')" />
                <has_line_matching expression="S5=c\(\d+\.\d+\)" />
              </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[
RPKM_saturation.py

In the output figure, Y axis is "Percent Relative Error" or "Percent Error" which is used
to measures how the RPKM estimated from subset of reads (i.e. RPKMobs) deviates from real
expression level (i.e. RPKMreal). However, in practice one cannot know the RPKMreal. As a
proxy, we use the RPKM estimated from total reads to approximate RPKMreal.

.. image:: http://rseqc.sourceforge.net/_images/RelativeError.png
   :height: 80 px
   :width: 400 px
   :scale: 100 %

Inputs

1. output..eRPKM.xls: RPKM values for each transcript
2. output.rawCount.xls: Raw count for each transcript
3. output.saturation.r: R script to generate plot
4. output.saturation.pdf:

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

- All transcripts were sorted in ascending order according to expression level (RPKM). Then they are divided into 4 groups:

    x <- seq(5,100,5)  #resampling percentage (5,10,15,...,100)
    rpkm <- c(32.95,35.43,35.15,36.04,36.41,37.76,38.96,38.62,37.81,38.14,37.97,38.58,38.59,38.54,38.67, 38.67,38.87,38.68,  38.42,  38.23)  #Paste RPKM values calculated from each subsets
    scatter.smooth(x,100*abs(rpkm-rpkm[length(rpkm)])/(rpkm[length(rpkm)]),type="p",ylab="Precent Relative Error",xlab="Resampling Percentage")
    dev.off()          #close graphical device

.. image:: http://rseqc.sourceforge.net/_images/saturation_eg.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_RPKM_saturation" name="RPKM Saturation" version="@WRAPPER_VERSION@">
    <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description>

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

    <expand macro="requirements" />

    <expand macro="stdio" />

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

    <command><![CDATA[
        RPKM_saturation.py -i '${input}' -o output -r '${refgene}'

        #if str($strand_type.strand_specific) == "pair"
            -d
            #if str($strand_type.pair_type) == "sd"
                '1++,1--,2+-,2-+'

            #else
                '+-,-+'
            #end if
        #end if

        -l ${percentileFloor} -u ${percentileCeiling} -s ${percentileStep} -c ${rpkmCutoff}
        ]]>
    </command>

    <inputs>
        <expand macro="bam_param" />
        <expand macro="refgene_param" />
        <expand macro="strand_type_param" />
        <param name="percentileFloor" type="integer" value="5" label="Begin sampling from this percentile (default=5)" help="(--percentile-floor)"/>
        <param name="percentileCeiling" type="integer" value="100" label="End sampling at this percentile (default=100)" help="(--percentile-ceiling)" />
        <param name="percentileStep" type="integer" value="5" label="Sampling step size (default=5)" help="(--percentile-step)" />
        <param name="rpkmCutoff" type="text" value="0.01" label="Ignore transcripts with RPKM smaller than this number (default=0.01)" help="(--rpkm-cutoff)" />
        <expand macro="mapq_param" />
        <expand macro="rscript_output_param" />
    </inputs>

    <outputs>
        <expand macro="pdf_output_data" filename="output.saturation.pdf" />
        <data format="xls" name="outputxls" from_work_dir="output.eRPKM.xls" label="${tool.name} on ${on_string} (RPKM xls)"/>
        <data format="xls" name="outputrawxls" from_work_dir="output.rawCount.xls" label="${tool.name} on ${on_string} (Raw Count xls)"/>
        <expand macro="rscript_output_data" filename="output.saturation.r" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
            <param name="refgene" value="hg19.HouseKeepingGenes_30.bed"/>
            <param name="rscript_output" value="true" />
            <output name="outputxls">
              <assert_contents>
                <has_n_columns n="26" />
                <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" />
              </assert_contents>

              <assert_contents>
                <has_text text="pdf('output.saturation.pdf')" />
                <has_line_matching expression="S5=c\(\d+\.\d+\)" />
              </assert_contents>
            </output>
            <output name="outputpdf" file="output.saturation.pdf" compare="sim_size" />
        </test>
    </tests>

    <help><![CDATA[
RPKM_saturation.py

In the output figure, Y axis is "Percent Relative Error" or "Percent Error" which is used
to measures how the RPKM estimated from subset of reads (i.e. RPKMobs) deviates from real
expression level (i.e. RPKMreal). However, in practice one cannot know the RPKMreal. As a
proxy, we use the RPKM estimated from total reads to approximate RPKMreal.

.. image:: $PATH_TO_IMAGES/RelativeError.png
   :height: 80 px
   :width: 400 px
   :scale: 100 %

Inputs

1. output..eRPKM.xls: RPKM values for each transcript
2. output.rawCount.xls: Raw count for each transcript
3. output.saturation.r: R script to generate plot
4. output.saturation.pdf:

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

- All transcripts were sorted in ascending order according to expression level (RPKM). Then they are divided into 4 groups:

    x <- seq(5,100,5)  #resampling percentage (5,10,15,...,100)
    rpkm <- c(32.95,35.43,35.15,36.04,36.41,37.76,38.96,38.62,37.81,38.14,37.97,38.58,38.59,38.54,38.67, 38.67,38.87,38.68,  38.42,  38.23)  #Paste RPKM values calculated from each subsets
    scatter.smooth(x,100*abs(rpkm-rpkm[length(rpkm)])/(rpkm[length(rpkm)]),type="p",ylab="Precent Relative Error",xlab="Resampling Percentage")
    dev.off()          #close graphical device

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

@ABOUT@

]]>
    </help>

    <expand macro="citations" />