comparison plotProfiler.xml @ 6:e6dbb616211e draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41

5:f30699e4e902

            --outFileName "$outFileName"

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

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

                #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:

                    <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 comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>

                <expand macro="plotTitle" />

                    The color names should be given 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 the region file contains groups separated by &quot;#&quot;,
                    plot the groups next to each other. The default is to plot the samples next to each other.
                    If this option is set, each group (or cluster) will get its own plot, with different samples
                    stacked on top of 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"

.. 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/release-1.6/content/tools/plotProfile.html


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@REFERENCES@

6:e6dbb616211e

            --outFileName "$outFileName"

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

                #if $output.saveData:
                    --outFileNameData "$outFileNameData"
                #end if

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

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

                $advancedOpt.onePlotPerGroup

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

                    <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="genes" 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 comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>

                <expand macro="plotTitle" />

                    The color names should be given 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="--onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
                    label="Do one plot per group"
                    help="When the region file contains groups separated by &quot;#&quot;, the default is
                    to plot the averages for the distinct plots in one plot. If this option is set, each group
                    will get its own plot, stacked on top of 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"

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


You can find more details on the profiler wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler


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@REFERENCES@