comparison hicPlotDistVsCounts.xml @ 18:e2971589184b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"

17:c8a6f89921dc

<tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>compute distance vs Hi-C counts plot per chromosome</description>
    <macros>
        <token name="@BINARY@">hicPlotDistVsCounts</token>
        <import>macros.xml</import>
    </macros>

                $outFileData_Boolean ./outFileData
            #end if
]]>
    </command>
    <inputs>
        <param argument="--matrices" type="data" format="h5,cool" multiple="True" label="Hi-C corrected matrices"/>

        <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts"
            help="If set, diagonal counts are not included"/>
        <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome"
            help="If more than one Hi-C matrix is given for each chromosome a new plot is made. Otherewise, a single plot with one line per chromosome is created." />
        <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth"
            help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." />
        <param argument="--plotsize" type="text" optional="True" label="Plot size"
            help="Width and height of the plot (in inches). Default is 6 * number of cols, 4 * number of rows. The maximum number of rows is 4. Example: 6 5." />
        <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude"
            help="This is useful for example to exclude the Y chromosome or to reduce the analysis to only a few chromosomes.">
            <param argument="--chromosomeExclude" type="text" value="" >
                <validator type="empty_field" />
            </param>
        </repeat>
        <param name='outFileData_Boolean' type='boolean' truevalue='--outFileData'  falsevalue="" checked="false" label="Save data underlying the plots as BAM"
            help="A bam file containing all data underlying the plots is saved on this file."/>
    </inputs>
    <outputs>
        <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot"/>
        <data name="outFileData" from_work_dir="outFileData" format="txt" label="${tool.name} data file on ${on_string}">
            <filter>outFileData_Boolean</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrices" ftype="h5" value="small_test_matrix.h5"/>
            <param name="skipDiagonal" value="False"/>
            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrices" ftype="h5" value="small_test_matrix.h5"/>
            <param name="skipDiagonal" value="False"/>
            <param name='outFileData_Boolean' value='True'/>
            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
            <output name="outFileData" file="distVsCounts.txt" ftype="txt" compare="sim_size" delta='600'/>
        </test>
        <test>
            <param name="matrices" ftype="h5" value="small_test_matrix.h5,small_test_matrix.h5"/>
            <param name="skipDiagonal" value="False"/>
            <param name="perchr" value="True" />
            <repeat name="chromosomeExclude">
                <param name="chromosomeExclude" value="chrUextra"/>
            </repeat>
            <repeat name="chromosomeExclude">
                <param name="chromosomeExclude" value="chrM"/>
            </repeat>
            <repeat name="chromosomeExclude">
                <param name="chromosomeExclude" value="chr3LHet"/>
            </repeat>
            <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="40000"/>
        </test>
    </tests>
    <help><![CDATA[
Relation of genomic distance and number of contacts
===================================================

**hicPlotDistVsCounts** allows a quick comparison between multiple Hi-C matrices of the Hi-C counts enrichment at different genomic ranges / distances up to whole chromosome. Biological replicates should display the exact same distribution while samples coming from different cell-lines, treated versus untreated samples or mutant versus wild-type samples should display a different distribution at long and/or close range.

_________________

| For more information about HiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
]]></help>
    <expand macro="citations" />
</tool>

18:e2971589184b

<tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>compute distance vs Hi-C counts plot per chromosome</description>
    <macros>
        <token name="@BINARY@">hicPlotDistVsCounts</token>
        <import>macros.xml</import>
    </macros>

                $outFileData_Boolean ./outFileData
            #end if
]]>
    </command>
    <inputs>
        <param argument="--matrices" type="data" format="h5,cool" multiple="True" label="Hi-C corrected matrices" />

        <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" help="If set, diagonal counts are not included" />
        <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome" help="If more than one Hi-C matrix is given for each chromosome a new plot is made. Otherewise, a single plot with one line per chromosome is created." />
        <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth" help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." />
        <param argument="--plotsize" type="text" optional="True" label="Plot size" help="Width and height of the plot (in inches). Default is 6 * number of cols, 4 * number of rows. The maximum number of rows is 4. Example: 6 5.">
            <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
        </param>
        <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude" help="This is useful for example to exclude the Y chromosome or to reduce the analysis to only a few chromosomes.">
            <param argument="--chromosomeExclude" type="text" value="">
                <validator type="empty_field" />
            </param>
        </repeat>
        <param name='outFileData_Boolean' type='boolean' truevalue='--outFileData' falsevalue="" checked="false" label="Save data underlying the plots as BAM" help="A bam file containing all data underlying the plots is saved on this file." />
    </inputs>
    <outputs>
        <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot" />
        <data name="outFileData" from_work_dir="outFileData" format="txt" label="${tool.name} data file on ${on_string}">
            <filter>outFileData_Boolean</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrices" ftype="h5" value="small_test_matrix.h5" />
            <param name="skipDiagonal" value="False" />
            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size" />
        </test>
        <test>
            <param name="matrices" ftype="h5" value="small_test_matrix.h5" />
            <param name="skipDiagonal" value="False" />
            <param name='outFileData_Boolean' value='True' />
            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size" />
            <output name="outFileData" file="distVsCounts.txt" ftype="txt" />
        </test>
        <test>
            <param name="matrices" ftype="h5" value="small_test_matrix.h5,small_test_matrix.h5" />
            <param name="skipDiagonal" value="False" />
            <param name="perchr" value="True" />
            <repeat name="chromosomeExclude">
                <param name="chromosomeExclude" value="chrUextra" />
            </repeat>
            <repeat name="chromosomeExclude">
                <param name="chromosomeExclude" value="chrM" />
            </repeat>
            <repeat name="chromosomeExclude">
                <param name="chromosomeExclude" value="chr3LHet" />
            </repeat>
            <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[

Relation of genomic distance and number of contacts
===================================================

**hicPlotDistVsCounts** allows a quick comparison between multiple Hi-C matrices of the Hi-C counts enrichment at different genomic ranges / distances up to whole chromosome. Biological replicates should display the exact same distribution while samples coming from different cell-lines, treated versus untreated samples or mutant versus wild-type samples should display a different distribution at long and/or close range.

_________________

| For more information about HiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
]]>    </help>
    <expand macro="citations" />
</tool>