view plotProfiler.xml @ 10:0c6e6cadd59d draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'28834090962775526c1a6d7e7f6515b134483d3e'

<tool id="deeptools_plot_profile" name="plotProfile" version="@WRAPPER_VERSION@.0">
    <description>
        creates a profile plot for a score associated to genomic regions
    </description>
    <macros>
        <token name="@BINARY@">plotProfile</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[
        @BINARY@
            --matrixFile "$matrixFile"
            --outFileName "$outFileName"

            #if $output.showOutputSettings == "yes"
                --plotFileFormat $output.outFileFormat

                #if $output.saveSortedRegions:
                    --outFileSortedRegions '$outFileSortedRegions'
                #end if
            #else
                --plotFileFormat 'png'
            #end if

            #if $scaleRegions.showScaleRegionsOpt == "yes":
                --startLabel '$scaleRegions.startLabel'
                --endLabel '$scaleRegions.endLabel'
            #end if

            #if $advancedOpt.showAdvancedOpt == "yes":
                #if $advancedOpt.averageType:
                    --averageType '$advancedOpt.averageType'
                #end if
                --plotHeight $advancedOpt.plotHeight
                --plotWidth $advancedOpt.plotWidth
                --plotType $advancedOpt.plotType
                --regionsLabel '$advancedOpt.regionsLabel'

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

                #if str($advancedOpt.colors).strip() != "":
                    --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
                #end if

                $advancedOpt.perGroup

                #if $advancedOpt.yMin:
                    --yMin $advancedOpt.yMin
                #end if
                #if $advancedOpt.yMax:
                    --yMax $advancedOpt.yMax
                #end if

                @KMEANS_CLUSTERING@

            #end if
]]>
    </command>
    <inputs>
        <param argument="--matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
        <conditional name="scaleRegions">
            <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode">
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param argument="--startLabel" type="text" value="TSS" size="10"
                    label="Label for the region start"
                    help ="Label shown in the plot
                    for the start of the region. Default is TSS (transcription start site),
                    but could be changed to anything, e.g. &quot;peak start&quot;." />
                <param argument="--endLabel" type="text" value="TES" size="10"
                    label="Label for the region end"
                    help="Label shown in the plot for the region end. Default is TES (transcription end site)."/>
            </when>
        </conditional>

        <expand macro="input_graphic_output_settings">
            <expand macro="input_image_file_format" />
        </expand>

        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param name="averageType" type="select" label="Define the type of statistic that should be used for the profile.">
                    <option value="mean" selected="true">mean</option>
                    <option value="median">median</option>
                    <option value="min">min</option>
                    <option value="max">max</option>
                    <option value="sum">sum</option>
                    <option value="std">std</option>
                </param>
                <param argument="--plotHeight" type="integer" value="5" min="3"
                    label="Plot height"
                    help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />

                <param argument="--plotWidth" type="integer" value="8" min="1"
                    label="Plot width"
                    help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />

                <param argument="--plotType" type="select" label="Plot type"
                    help="The &quot;lines&quot; option will
                    plot the profile line based on the average type selected. The &quot;fill&quot;
                    option fills the region between zero and the profile curve. The filled in color is
                    semi-transparent. The &quot;add standard error&quot;
                    option colors the region between the profile and the standard error of the data.
                    As in the case of fill, a semi-transparent color is used.
                    The option &quot;overlapped_lines&quot; plots each region's value, one on top of
                    the other.">
                    <option value="lines" selected="true">lines</option>
                    <option value="fill">fill</option>
                    <option value="se">add standard error</option>
                    <option value="overlapped_lines">overlapped lines</option>
                </param>
                <param argument="--regionsLabel" type="text" value="coverage" size="30"
                    label="Labels for the regions plotted in the heatmap"
                    help="If more than one region is being plotted a list of labels separated
                    by commas is required. For example, &quot;label1, label2&quot;."/>

                <expand macro="plotTitle" />
                <param argument="--colors" type="text" value="" size="40"
                    label="List of colors to use for the plotted lines"
                    help="Color names and html hex strings (e.g. #eeff22) are accepted.
                    The color names should be separated by spaces. (--colors red blue green)">
                    <validator type="expression"
                        message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
                </param>

                <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
                    label="Do one plot per group"
                    help="When clustering is applied to the data or multiple BED files were used,
                    plot the groups next to each other. The default is to plot the samples next to each other." />


                <param argument="--yMin" type="float" value="" size="3" optional="true"
                    label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
                <param argument="--yMax" type="float" value="" size="3" optional="true"
                    label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" />

                <expand macro="kmeans_clustering" />

            </when>
        </conditional>
    </inputs>
    <outputs>
        <expand macro="output_image_file_format" />
        <expand macro="output_graphic_outputs" />
    </outputs>
    <tests>
        <test>
            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
            <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="4000" />
        </test>
        <test>
            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="showScaleRegionsOpt" value="yes" />
            <output name="outFileName" file="profiler_result2.png" ftype="png" compare="sim_size" delta="4000" />
        </test>
    </tests>
    <help>
<![CDATA[

**What it does**

This tool plots the average enrichments over all genomic
regions supplied to computeMarix. It requires that computeMatrix was successfully run.
It is a very useful complement to the heatmapper, especially in cases where you want to
compare the scores for many different groups. Like heatmapper, profiler does not change the
values that were compute by computeMatrix, but you can modify the color and other display properties of the plots.


.. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png
   :alt: Meta-gene profile of Rna Polymerase II


You can find more details on the profiler doc page: https://deeptools.readthedocs.org/en/master/content/tools/plotProfile.html


-----

@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>