comparison deepTools_macros.xml @ 2:1f0bbd337f21 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829

1:7d3d567c5b67

            --zMin $zMin
        #end if
        #if $zMax:
            --zMax $zMax
        #end if
            --colorMap '$colorMap'
        $plotNumbers
    </token>

        <expand macro="plotTitle" />
        <expand macro="plotNumbers" />
        <conditional name="output">
            <param name="showOutputSettings" type="select" label="Show advanced output settings" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <expand macro="input_image_file_format"/>
                <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
                <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
            </when>
        </conditional>

    <xml name="includeZeros">
        <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
            label="Include zeros"
            help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." />

    </xml>


    <xml name="kmeans_clustering">
        <conditional name="used_multiple_regions">
            <param name="used_multiple_regions_options" type="select" 
                label="Did you compute the matrix with more than one groups of regions?"
                help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
                <option value="yes">Yes, I used multiple groups of regions</option>
                <option value="no">No, I used only one group</option>
            </param>

                    <param name="clustering_options" type="select" label="Clustering algorithm">
                        <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>

        <expand macro="samFlags" />
    </xml>

    <xml name="plotNumbers">
        <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
            label="Plot the correlation value" 
            help="If set, then the correlation number is plotted on top of the heatmap."/>
    </xml>

    <xml name="extendReads">
        <param argument="--extendReads" type="integer" value="" optional="True"

If you would like to give us feedback or you run into any trouble, please send an email to [e-mail]

This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.

.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
.. _help site: https://github.com/fidelram/deepTools/wiki/

    </token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/nar/gku365</citation>

            help="The BAM file must be sorted."/>
    </xml>

    <xml name="multiple_input_bigwigs">
        <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True"
            label="Bigwig file" 
            help="The Bigwig file must be sorted."/>
    </xml>

    <xml name="plotTitle">
        <param argument="--plotTitle" type="text" value="" size="30" optional="True"

    </token>

    <xml name="effectiveGenomeSize">
        <conditional name="effectiveGenomeSize">
            <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
                help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. 
                    Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. 
                    See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
                <option value="93260000">ce10 (93260000)</option>
                <option value="121400000">dm3 (121400000)</option>
                <option value="2451960000" selected="true">hg19 (2451960000)</option>
                <option value="2150570000">mm9 (2150570000)</option>

    <xml name="output_save_matrix_values">
        <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and 
                output['saveMatrix'] is True
            ))
            </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
            ))
            </filter>
        </data>
    </xml>

2:1f0bbd337f21

            --zMin $zMin
        #end if
        #if $zMax:
            --zMax $zMax
        #end if
        --colorMap '$colorMap'
        $plotNumbers
        --plotTitle $plotTitle
    </token>


    <xml name="includeZeros">
        <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
            label="Include zeros"
            help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." />

    </xml>


    <xml name="kmeans_clustering">
        <conditional name="used_multiple_regions">
            <param name="used_multiple_regions_options" type="select"
                label="Did you compute the matrix with more than one groups of regions?"
                help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
                <option value="yes">Yes, I used multiple groups of regions</option>
                <option value="no">No, I used only one group</option>
            </param>

                    <param name="clustering_options" type="select" label="Clustering algorithm">
                        <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>

        <expand macro="samFlags" />
    </xml>

    <xml name="plotNumbers">
        <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
            label="Plot the correlation value"
            help="If set, then the correlation number is plotted on top of the heatmap."/>
    </xml>

    <xml name="extendReads">
        <param argument="--extendReads" type="integer" value="" optional="True"

If you would like to give us feedback or you run into any trouble, please send an email to [e-mail]

This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.

.. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
.. _help site: https://deeptools.readthedocs.org/

    </token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/nar/gku365</citation>

            help="The BAM file must be sorted."/>
    </xml>

    <xml name="multiple_input_bigwigs">
        <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True"
            label="Bigwig file"
            help="The Bigwig file must be sorted."/>
    </xml>

    <xml name="plotTitle">
        <param argument="--plotTitle" type="text" value="" size="30" optional="True"

    </token>

    <xml name="effectiveGenomeSize">
        <conditional name="effectiveGenomeSize">
            <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
                help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
                    Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
                    See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
                <option value="93260000">ce10 (93260000)</option>
                <option value="121400000">dm3 (121400000)</option>
                <option value="2451960000" selected="true">hg19 (2451960000)</option>
                <option value="2150570000">mm9 (2150570000)</option>

    <xml name="output_save_matrix_values">
        <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and
                output['saveMatrix'] is True
            ))
            </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
            ))
            </filter>
        </data>
    </xml>