comparison plotProfiler.xml @ 8:4339a4d28e97 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7

7:a6d65190c7e5

            </param>
            <when value="no" />
            <when value="yes">
                <param argument="--startLabel" type="text" value="TSS" size="10"
                    label="Label for the region start"
                    help ="[only for scale-regions mode] 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)."/>

                <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="For the summary plot (profile) only. 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 fill in color is
                    semi transparent to distinguish different profiles. 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 values, one on top of
                    the other; this option only works if &quot;one plot per proup&quot; is set.">
                    <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" />
                <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 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"

**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 when 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 choose between
many different ways to color and display the plots.


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

8:4339a4d28e97

            </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)."/>

                <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"

**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