comparison deepTools_macros.xml @ 6:d2e4ebf1ce32 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 8b9cdb8dc4a8fedd2b2286e7afab6529e49a9d22-dirty

5:67a321b21481

        <expand macro="plotTitle" />
        <expand macro="plotNumbers" />
    </xml>

    <token name="@HEATMAP_OPTIONS@">
        #if $plotting_type.zMin:
            --zMin $plotting_type.zMin
        #end if
        #if $plotting_type.zMax:
            --zMax $plotting_type.zMax
        #end if
        --colorMap '$plotting_type.colorMap'
        $plotting_type.plotNumbers
        --plotTitle '$plotting_type.plotTitle'

                        <option value="none">No clustering</option>
                        <option value="kmeans">Kmeans clustering</option>
                    </param>
                    <when value="kmeans">
                        <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
                            help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
                    </when>
                    <when value="none" />
                </conditional>
            </when>
            <when value="yes" />

                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <yield />
                <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
                <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
            </when>
        </conditional>
    </xml>

            </filter>
        </data>
    </xml>

    <xml name="output_graphic_outputs">
        <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and
                output['saveData'] is True
            ))
            </filter>
        </data>
        <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and
                output['saveSortedRegions'] is True

6:d2e4ebf1ce32

        <expand macro="plotTitle" />
        <expand macro="plotNumbers" />
    </xml>

    <token name="@HEATMAP_OPTIONS@">
        #if str($plotting_type.zMin) != "":
            --zMin $plotting_type.zMin
        #end if
        #if str($plotting_type.zMax) != "":
            --zMax $plotting_type.zMax
        #end if
        --colorMap '$plotting_type.colorMap'
        $plotting_type.plotNumbers
        --plotTitle '$plotting_type.plotTitle'

                        <option value="none">No clustering</option>
                        <option value="kmeans">Kmeans clustering</option>
                    </param>
                    <when value="kmeans">
                        <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
                            help="When this option is set, then the matrix is split into clusters using the kmeans algorithm.
                            Only works for data that is not grouped, otherwise only the first group will be clustered.
                            If more specific clustering methods are required it is advisable to save the underlying matrix and
                            run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault)
                            if a cluster has very few members compared to the total number or regions. (default: 0 [do not cluster])."/>
                    </when>
                    <when value="none" />
                </conditional>
            </when>
            <when value="yes" />

                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <yield />
                <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
            </when>
        </conditional>
    </xml>

            </filter>
        </data>
    </xml>

    <xml name="output_graphic_outputs">
        <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and
                output['saveSortedRegions'] is True