comparison bam2wig.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_bam2wig" name="BAM to Wiggle" version="2.4galaxy1">
    <description>
        converts all types of RNA-seq data from .bam to .wig
    </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[bam2wig.py --version]]></version_command>

    <command><![CDATA[
        ln -sfn '${input}' 'input.bam' &&
        ln -sfn '${input.metadata.bam_index}' 'input.bam.bai' &&
        bam2wig.py -i input.bam -s $chromsize -o outfile

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

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

        #if $wigsum.wigsum_type
            -t $wigsum.totalwig
        #end if
        #if $multihits.skipmultihits
            --skip-multi-hits
            --mapq=$multihits.mapq
        #end if
        2>&1
        ]]>
    </command>
    <inputs>
        <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
        <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" help="(--chromSize)"/>

        <conditional name="multihits">
            <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" help="(--skip-multi-hits)" />
            <when value="true">
                <param name="mapq" value="30" type="integer" label="Minimum mapping quality for an alignment to be called 'uniquly mapped'" help="(--mapq)" />
            </when>
            <when value="false" />
        </conditional>

        <conditional name="wigsum">
            <param name="wigsum_type" type="boolean" label="Specify wigsum?" value="false">
            </param>
            <when value="true">
                <param name="totalwig" value="0" type="integer" label="specified wigsum" help="(--wigsum)"/>
            </when>
            <when value="false"/>
        </conditional>

        <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>
    </inputs>

    <outputs>
        <data format="wig" name="output" from_work_dir="outfile.wig">
            <filter>strand_type['strand_specific'] == 'none'</filter>

            <output name="output" file="testwig.wig"/>
        </test>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <param name="chromsize" value="hg19.chrom.sizes"/>
            <param name="skipmultihits" value="True"/>
            <param name="mapq" value="20"/>
            <output name="output" file="testwig.wig"/>
        </test>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <param name="chromsize" value="hg19.chrom.sizes"/>

++++++++++++++

If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq
is strand specific, two wig files corresponding to Forward and Reverse will be generated.

-----

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/

.. _UCSC: http://genome.ucsc.edu/index.html
.. _IGB: http://bioviz.org/igb/
.. _IGV: http://www.broadinstitute.org/igv/home
.. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html
.. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
.. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
]]>
    </help>

51:09846d5169fa

<tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@WRAPPER_VERSION@">
    <description>
        converts all types of RNA-seq data from .bam to .wig
    </description>

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

    <expand macro="requirements" />

    <expand macro="stdio" />

    <version_command><![CDATA[bam2wig.py --version]]></version_command>

    <command><![CDATA[
        ln -sf '${input}' 'input.bam' &&
        ln -sf '${input.metadata.bam_index}' 'input.bam.bai' &&
        bam2wig.py -i 'input.bam' -s '${chromsize}' -o outfile

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

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

        #if str($wigsum_type.wigsum_type_selector) == "normalize":
            -t ${wigsum.totalwig}
        #end if

        @MULTIHITS@
        ]]>
    </command>
    <inputs>
        <expand macro="bam_param" />
        <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" help="(--chromSize)"/>
        <expand macro="multihits_param" />
        <conditional name="wigsum_type">
            <param name="wigsum_type_selector" type="select" label="Normalization">
                <option value="normalize">Normalize to specified sum</option>
                <option value="raw" selected="true">Do not normalize</option>
            </param>
            <when value="normalize">
                <param name="totalwig" value="" type="integer" label="specified wigsum" help="(--wigsum)"/>
            </when>
            <when value="raw"/>
        </conditional>
        <expand macro="strand_type_param" />
    </inputs>

    <outputs>
        <data format="wig" name="output" from_work_dir="outfile.wig">
            <filter>strand_type['strand_specific'] == 'none'</filter>

            <output name="output" file="testwig.wig"/>
        </test>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <param name="chromsize" value="hg19.chrom.sizes"/>
            <param name="multihits_type.multihits_type_selector" value="skipmultihits"/>
            <param name="multihits_type.mapq" value="20"/>
            <output name="output" file="testwig.wig"/>
        </test>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <param name="chromsize" value="hg19.chrom.sizes"/>

++++++++++++++

If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq
is strand specific, two wig files corresponding to Forward and Reverse will be generated.

@ABOUT@

.. _UCSC: http://genome.ucsc.edu/index.html
.. _IGB: http://bioviz.org/igb/
.. _IGV: http://software.broadinstitute.org/software/igv/
.. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html
.. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
.. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
]]>
    </help>