comparison deepTools_macros.xml @ 7:44d87fb8403e draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

6:7cbaaf80dced

        <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

7:44d87fb8403e

        <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