comparison deepTools_macros.xml @ 1:011ea45dda07 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920

0:bb2b0ad44c0e

            label="Region of the genome to limit the operation to"
            help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." />
    </xml>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.0.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.7.10">python</requirement>
            <requirement type="binary">@BINARY@</requirement>
            <requirement type="package" version="2.0.1">deepTools</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

            <when value="no">
                <conditional name="clustering">
                    <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, the matrix is split into clusters using the k-means algorithm.
                            This 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."/>
                    </when>
                    <when value="none" />
                </conditional>
            </when>
            <when value="yes" />
        </conditional>

    <token name="@KMEANS_CLUSTERING@">
        #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
                #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
                    --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
                #end if
            #end if
        #end if
    </token>

            <yield />
        </citations>
    </xml>

    <xml name="multiple_input_bams">
        <param argument="--bamfiles" type="data" format="bam" min="2"
            label="Bam file" multiple="true"
            help="The BAM file must be sorted."/>
    </xml>

    <xml name="plotTitle">
        <param argument="--plotTitle" type="text" value="" size="30" optional="True"
            label="Title of the plot"
            help="Title of the plot, to be printed on top of the generated image." />
    </xml>

    <token name="@multiple_input_bams@">
<![CDATA[
        #set files=[]
        #set labels=[]

1:011ea45dda07

            label="Region of the genome to limit the operation to"
            help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." />
    </xml>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.1.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.7.10">python</requirement>
            <requirement type="binary">@BINARY@</requirement>
            <requirement type="package" version="2.1.0">deepTools</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

            <when value="no">
                <conditional name="clustering">
                    <param name="clustering_options" type="select" label="Clustering algorithm">
                        <option value="none">No clustering</option>
                        <option value="kmeans">Kmeans clustering</option>
                        <option value="hclust">Hierarchical 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, the matrix is split into clusters using the k-means algorithm.
                            This 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."/>
                    </when>
                    <when value="hclust">
                        <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
                            help="WARNING: This option causes the tool to run for a very long time! When this option is
                            set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
                            This only works for data that is not grouped, otherwise only the first group will be clustered.
                            Note that you must have used the '--missingDataAsZero' option within computeMatrix!
                            If more specific clustering methods are required it is advisable to save the underlying matrix and
                            run the clustering using other software."/>
                    </when>
                    <when value="none" />
                </conditional>
            </when>
            <when value="yes" />
        </conditional>

    <token name="@KMEANS_CLUSTERING@">
        #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
                #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
                    --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
                #end if
            #end if
            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
                #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
                    --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
                #end if
            #end if
        #end if
    </token>

            <yield />
        </citations>
    </xml>

    <xml name="multiple_input_bams">
        <param argument="--bamfiles" type="data" format="bam" min="1"
            label="Bam file" multiple="true"
            help="The BAM file must be sorted."/>
    </xml>

    <xml name="multiple_input_bams_min2">
        <param argument="--bamfiles" type="data" format="bam" min="2"
            label="Bam file" multiple="true"
            help="The BAM file must be sorted."/>
    </xml>

    <xml name="plotTitle">
        <param argument="--plotTitle" type="text" value="" size="30" optional="True"
            label="Title of the plot"
            help="Title of the plot, to be printed on top of the generated image." />
    </xml>


    <token name="@multiple_input_bams@">
<![CDATA[
        #set files=[]
        #set labels=[]