comparison hicPlotMatrix.xml @ 15:4053214bebac draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"

14:162d027d61bf

    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        #if str($pca_conditional.pca_type) == 'bigwig':
            ln -s $pca_conditional.pca_bigwig pca.bw &&
            #set $pca = '--bigwig pca.bw'
        #elif str($pca_conditional.pca_type) == '':
            #set $pca = ''
        #end if

        @BINARY@

            --matrix '$matrix_h5_cooler'

            #if $title and $title is not None:
                --title '$title'
            #end if

            $perChromosome
            $clearMaskedBins

            ## special: --chromosomeOrder is optional, but if given needs at least one argument
            #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ])
            #if chroms:
                --chromosomeOrder "$chroms"
            #end if

            #if $region:

            #end if

            #if $vMax:
                --vMax $vMax
            #end if

            $pca

        && mv plot.$image_file_format plot
]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />

            </param>
            <when value='' />
            <when value='bigwig'>
                <param name='pca_bigwig'  type="data" format="bigwig"
                            label="Eigenvector file"/>
            </when>
        </conditional>
        <param name="image_file_format" type="select" label="Image output format">
            <option value="png" selected="True">png</option>
            <option value="svg">svg</option>
        </param>
    </inputs>
    <outputs>
        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
            <change_format>
                <when input="image_file_format" value="svg" format="svg" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
            <conditional name="pca_conditional">
                <param name="pca_type" value=''/>
            </conditional>
            <param name="region" value="chrX:3000000-3500000"/>
            <param name="region2" value="chrX:3100000-3600000"/>
            <param name="log1p" value="True"/>
            <param name="clearMaskedBins" value="True"/>
            <param name="image_file_format" value="png" />
            <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="Li_et_al_2015.cool"/>
            <conditional name="pca_conditional">
                <param name="pca_type" value=''/>
            </conditional>
            <param name="region" value="X:3000000-3500000"/>
            <param name="image_file_format" value="png" />
            <output name="outFileName" file="Li_chrX30-35_cool.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="pearson_small_50kb.cool"/>
            <param name="perChromosome" value="True"/>
            <conditional name="pca_conditional">
                <param name="pca_type" value='bigwig'/>
                <param name="pca_bigwig" value="pca1.bw"/>
            </conditional>
            <param name='colormap' value='hot'/>
            <param name="image_file_format" value="svg" />
            <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="pearson_small_50kb.h5"/>
            <param name="perChromosome" value="True"/>
            <conditional name="pca_conditional">
                <param name="pca_type" value='bigwig'/>
                <param name="pca_bigwig" value="pca1.bw"/>
            </conditional>
            <param name='colormap' value='hot'/>

            <param name="image_file_format" value="svg" />
            <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/>
        </test>
    </tests>
    <help><![CDATA[
Contact matrix plot
=======================

15:4053214bebac

    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        #if str($pca_conditional.pca_type) == 'bigwig':
            ln -s '$pca_conditional.pca_bigwig' pca.bw &&
            #set $pca = '--bigwig pca.bw'
        #elif str($pca_conditional.pca_type) == '':
            #set $pca = ''
        #end if
        ln -s $matrix_h5_cooler matrix.$matrix_h5_cooler.ext &&
        @BINARY@

            
            --matrix 'matrix.$matrix_h5_cooler.ext'

            #if $title and $title is not None:
                --title '$title'
            #end if

            $perChromosome
            $clearMaskedBins

            ## special: --chromosomeOrder is optional, but if given needs at least one argument
            #set chroms = ' '.join([ '\'' + str($var.chromosome) + '\'' for $var in $chromosomeOrder ])
            #if chroms:
                --chromosomeOrder "$chroms"
            #end if

            #if $region:

            #end if

            #if $vMax:
                --vMax $vMax
            #end if
            
            #if str($pca_conditional.pca_type) == 'bigwig':
                --vMinBigwig $pca_conditional.vMinBigwig
                --vMaxBigwig $pca_conditional.vMaxBigwig
                $pca_conditional.flipBigwigSign
                --scaleFactorBigwig $pca_conditional.scaleFactorBigwig
                $pca_conditional.bigwigAdditionalVerticalAxis
            #end if 
            $pca
            #if $dpi:
                --dpi $dpi
            #end if 

            #if $loops:
                --loops '$loops'
            #end if
        && mv plot.$image_file_format plot
]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />

            </param>
            <when value='' />
            <when value='bigwig'>
                <param name='pca_bigwig'  type="data" format="bigwig"
                            label="Eigenvector file"/>
                <param argument="--vMinBigwig" type="float" optional="true" label="vMinBigwig" help="Minimum value of the plotted bigwig score."/>
                <param argument="--vMaxBigwig" type="float" optional="true" label="vMaxBigwig" help="Maximum value of the plotted bigwig score."/>
                <param name='flipBigwigSign' type='boolean' optional="true" truevalue='--flipBigwigSign' falsevalue='' label='Flip the sign of the bigwig values' />
                <param argument="--scaleFactorBigwig" type="float" optional="true" label="Scale factor for bigwig" help="Scale the bigwig values by a factor."/>
                <param name='bigwigAdditionalVerticalAxis' type='boolean' optional="true" truevalue='--bigwigAdditionalVerticalAxis' falsevalue='' label='Plot an additional vertical axis.' />


            </when>
        </conditional>
        <param name='loops' type="data" format="interval" optional='True' label="Add detected loops"/>
        <param name="image_file_format" type="select" label="Image output format">
            <option value="png" selected="True">png</option>
            <option value="svg">svg</option>
            <option value="pdf">pdf</option>

        </param>
        <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
    </inputs>
    <outputs>
        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
            <change_format>
                <when input="image_file_format" value="svg" format="svg" />
                <when input="image_file_format" value="pdf" format="pdf" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
            <conditional name="pca_conditional">
                <param name="pca_type" value=''/>
            </conditional>
            <param name="region" value="chr2L:3000000-3500000"/>
            <param name="region2" value="chr2L:3100000-3600000"/>
            <param name="log1p" value="True"/>
            <param name="clearMaskedBins" value="True"/>
            <param name="image_file_format" value="png" />
            <param name="dpi" value="10" />

            <output name="outFileName" file="hicPlotMatrix/plot1.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
            <param name="region" value="chr2L:3000000-3500000"/>

            <conditional name="pca_conditional">
                <param name="pca_type" value=''/>
            </conditional>
            <param name="image_file_format" value="pdf" />
            <param name="dpi" value="10" />

            <output name="outFileName" file="hicPlotMatrix/plot2.pdf" ftype="pdf" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
            <conditional name="pca_conditional">
                <param name="pca_type" value='bigwig'/>
                <param name="pca_bigwig" value="hicPCA/pca1_test1.bw"/>
                <param name='vMinBigwig' value='10'/>
                <param name='vMaxBigwig' value='20'/>
                <param name='scaleFactorBigwig' value='2000'/>
                <param name='flipBigwigSign' value='True'/>
            </conditional>
            <param name='colormap' value='hot'/>
            <param name="region" value="chr2L:3000000-3500000"/>
            <param name="dpi" value="10" />

            <param name="image_file_format" value="svg" />
            <output name="outFileName" file="hicPlotMatrix/plot3_pca.svg" ftype="svg" compare="sim_size" delta="35000"/>
        </test>
        
    </tests>
    <help><![CDATA[
Contact matrix plot
=======================