comparison plotHeatmap.xml @ 17:0d6dfbd66443 draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty

16:4a42f2445e42

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

                #if str($advancedOpt.colorMap).strip() != "":
                    --colorMap #echo " ".join(str($advancedOpt.colorMap).strip().split(","))#
                #end if
                --alpha '$advancedOpt.alpha'
                #if str($advancedOpt.colorList).strip() != "":
                    --colorList $advancedOpt.colorList
                #end if

                #end if

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

                $advancedOpt.perGroup

                @KMEANS_CLUSTERING@

                    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." />

                <expand macro="colorMap" />
                <param argument="--alpha" type="float" value="1.0" min="0.0"
                    max="1.0" optional="True"
                    label="Alpha channel (transparency)"
                    help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must
                    be between 0 and 1. A value of 0.0 would be fully transparent." />

                    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" />
                <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."/>

                <expand macro="kmeans_clustering" />

17:0d6dfbd66443

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

                #set colorMap = []
                #for $cmap in $advancedOpt.colorMapRepeat:
                    #silent $colorMap.append(str($cmap.colorMap))
                #end for
                #if len($colorMap) > 0:
                    --colorMap #echo " ".join($colorMap)#
                #end if

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

                #end if

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

                --labelRotation '$advancedOpt.labelRotation'

                $advancedOpt.perGroup

                @KMEANS_CLUSTERING@

                    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." />

                <repeat name="colorMapRepeat" title="Colormap to use for each sample"
                    help="A different colormap can be applied to each column of the heatmap. If you select fewer colormaps than you have samples in your matrix, then the select colormap(s) will be repeated (e.g., if you select one colormap then it will be applied to all samples).">
                    <expand macro="colorMap" />
                </repeat>
                <param argument="--alpha" type="float" value="1.0" min="0.0"
                    max="1.0" optional="True"
                    label="Alpha channel (transparency)"
                    help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must
                    be between 0 and 1. A value of 0.0 would be fully transparent." />

                    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."/>

                <expand macro="kmeans_clustering" />