comparison plotHeatmap.xml @ 38:375e7508e571 draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d

37:7d1521817494

<tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@WRAPPER_VERSION@.0" profile="18.01">
    <description>creates a heatmap for score distributions across genomic regions</description>
    <macros>
        <token name="@BINARY@">plotHeatmap</token>
        <import>deepTools_macros.xml</import>
    </macros>

                #if $advancedOpt.averageTypeSummaryPlot:
                    --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
                #end if

                #if str($advancedOpt.missingDataColor.value) != "None":
                    --missingDataColor '$advancedOpt.missingDataColor'
                #end if

                #set colorMap = []

                --endLabel '$advancedOpt.endLabel'

                --refPointLabel '$advancedOpt.referencePointLabel'

                #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
                    --samplesLabel '$advancedOpt.samplesLabel'
                #end if

                #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
                    --regionsLabel '$advancedOpt.regionsLabel'
                #end if

                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
                    --plotTitle '$advancedOpt.plotTitle'
                #end if

                --labelRotation '$advancedOpt.labelRotation'

                $advancedOpt.perGroup

                    <option value="min">min</option>
                    <option value="max">max</option>
                    <option value="sum">sum</option>
                    <option value="std">std</option>
                </param>

                <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color"
                    help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
                    By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0).
                    Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
                    Alternatively colors can be specified using the #rrggbb notation." />

                    help="If more than one region is being plotted a list of labels separated by space is required.
                          If a label itself contains a space, then quotes are needed.
                          For example, label_1 "label 2"" />

                <expand macro="plotTitle" />
                <expand macro="labelRotation" />
                <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
                    label="Make one plot per group of regions"
                    help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."/>

38:375e7508e571

<tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@WRAPPER_VERSION@.1" profile="18.01">
    <description>creates a heatmap for score distributions across genomic regions</description>
    <macros>
        <token name="@BINARY@">plotHeatmap</token>
        <import>deepTools_macros.xml</import>
    </macros>

                #if $advancedOpt.averageTypeSummaryPlot:
                    --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
                #end if

                --plotType '$advancedOpt.plotType'

                #if str($advancedOpt.missingDataColor.value) != "None":
                    --missingDataColor '$advancedOpt.missingDataColor'
                #end if

                #set colorMap = []

                --endLabel '$advancedOpt.endLabel'

                --refPointLabel '$advancedOpt.referencePointLabel'

                #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
                    --samplesLabel $advancedOpt.samplesLabel
                #end if

                #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
                    --regionsLabel $advancedOpt.regionsLabel
                #end if

                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
                    --plotTitle '$advancedOpt.plotTitle'
                #end if

                --legendLocation '$advancedOpt.legendLocation'

                --labelRotation '$advancedOpt.labelRotation'

                $advancedOpt.perGroup

                    <option value="min">min</option>
                    <option value="max">max</option>
                    <option value="sum">sum</option>
                    <option value="std">std</option>
                </param>
                <param argument="--plotType" type="select" label="Type of summary plot">
                    <option value="lines">plot the profile line based on the statistic selected above.</option>
                    <option value="fill">fills the region between zero and the profile.</option>
                    <option value="se">color the region between the profile and the standard error.</option>
                    <option value="std">color the region between the profile and the standard deviation.</option>
                </param>
                <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color"
                    help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
                    By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0).
                    Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
                    Alternatively colors can be specified using the #rrggbb notation." />

                    help="If more than one region is being plotted a list of labels separated by space is required.
                          If a label itself contains a space, then quotes are needed.
                          For example, label_1 "label 2"" />

                <expand macro="plotTitle" />
                <expand macro="legendLocation" />
                <expand macro="labelRotation" />
                <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
                    label="Make one plot per group of regions"
                    help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."/>