comparison deepTools_macros.xml @ 9:f509604dbf06 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7

8:8ed7e3b6a16c

    <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="zMin_zMax">
        <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"
            help="If not specified the value is set automatically."/>

    </xml>

    <xml name="region_limit_operation">
        <param argument="--region" type="text" value=""
            label="Region of the genome to limit the operation to"
            help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;." />
    </xml>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.0.0</token>
    <xml name="requirements">

        <version_command>@BINARY@ --version</version_command>
    </xml>

    <xml name="smoothLength">
        <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
            label="Smooth values using the following length (in bp)"
            help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
    </xml>


    <xml name="kmeans_clustering">
        <conditional name="used_multiple_regions">

                        <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" />

    <xml name="extendReads">
        <conditional name="doExtendCustom">
            <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
                help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
                        By default *each* read mate is extended.
                        This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
                        Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value.
                        Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not
                        recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
                <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
                <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
                <option value="custom">A custom length, which will be applied to ALL reads.</option>
            </param>
            <when value="no" />

        <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
            label="Distance between bins"
            help="By default, bamCorrelate considers consecutive bins of
                the specified 'Bin size'. However, to reduce the
                computation time, a larger distance between bins can
                by given. Larger distances result in less bins being
                considered."/>
    </xml>

    <xml name="centerReads">
        <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
            label="Center regions with respect to the fragment length"
            help="For paired-end data, the read is centered at the fragment length defined by the two ends of the fragment. For single-end data, the given fragment length is used. This option is useful to get a sharper signal around enriched regions. "/>
    </xml>

    <xml name="ignoreDuplicates">
        <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
            label="Ignore duplicates"

    </xml>

    <xml name="minMappingQuality">
        <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
            label="Minimum mapping quality"
            help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
    </xml>

    <xml name="skipZeros">
        <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
            label ="Skip zeros"
            help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined." />
    </xml>

    <xml name="fragmentLength">
        <param argument="--fragmentLength" type="integer" value="300" min="1"
            label="Fragment length used for the sequencing"
            help ="If paired-end reads are used, the fragment length is computed from the BAM file."/>
    </xml>

    <xml name="scaleFactor">
        <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
            help="When used in combination with --normalizeTo1x or

    </xml>

    <xml name="multiple_input_bigwigs">
        <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
            label="Bigwig file"
            help="The Bigwig file must be sorted."/>
    </xml>

    <xml name="plotTitle">
        <param argument="--plotTitle" type="text" value="" size="30" optional="True"
            label="Title of the plot"

            help="This parameter determines if non-covered regions
                 (regions without overlapping reads) in a bam/bigWig file
                 should be skipped. The default is to treat those
                 regions as having a value of zero. The decision to
                 skip non-covered regions depends on the interpretation
                 of the data. Non-covered regions may represent for
                 example repetitive regions that want to be skipped.
                 (default: False)" />
    </xml>

    <xml name="input_save_matrix_values">
        <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>

9:f509604dbf06

    <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 are included. The default behavior is to ignore such regions." />
    </xml>

    <xml name="zMin_zMax">
        <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"
            help="If not specified the value is set automatically."/>

    </xml>

    <xml name="region_limit_operation">
        <param argument="--region" type="text" value=""
            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 &quot;chr10&quot; or &quot;chr10:456700:891000&quot;." />
    </xml>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.0.0</token>
    <xml name="requirements">

        <version_command>@BINARY@ --version</version_command>
    </xml>

    <xml name="smoothLength">
        <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
            label="Smooth values using the following length (in bases)"
            help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
    </xml>


    <xml name="kmeans_clustering">
        <conditional name="used_multiple_regions">

                        <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" />

    <xml name="extendReads">
        <conditional name="doExtendCustom">
            <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
                help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
                     By default *each* read mate is extended.
                     This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
                     Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
                     Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not
                     recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
                <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
                <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
                <option value="custom">A custom length, which will be applied to ALL reads.</option>
            </param>
            <when value="no" />

        <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
            label="Distance between bins"
            help="By default, bamCorrelate considers consecutive bins of
                the specified 'Bin size'. However, to reduce the
                computation time, a larger distance between bins can
                be given. Larger distances result in fewer bins being
                considered."/>
    </xml>

    <xml name="centerReads">
        <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
            label="Center regions with respect to the fragment length"
            help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/>
    </xml>

    <xml name="ignoreDuplicates">
        <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
            label="Ignore duplicates"

    </xml>

    <xml name="minMappingQuality">
        <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
            label="Minimum mapping quality"
            help= "If set, only reads with a mapping quality score higher than this value are considered."/>
    </xml>

    <xml name="skipZeros">
        <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
            label ="Skip zeros"
            help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." />
    </xml>

    <xml name="fragmentLength">
        <param argument="--fragmentLength" type="integer" value="300" min="1"
            label="Fragment length used for the sequencing"
            help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>
    </xml>

    <xml name="scaleFactor">
        <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
            help="When used in combination with --normalizeTo1x or

    </xml>

    <xml name="multiple_input_bigwigs">
        <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
            label="Bigwig file"
            help="A Bigwig file."/>
    </xml>

    <xml name="plotTitle">
        <param argument="--plotTitle" type="text" value="" size="30" optional="True"
            label="Title of the plot"

            help="This parameter determines if non-covered regions
                 (regions without overlapping reads) in a bam/bigWig file
                 should be skipped. The default is to treat those
                 regions as having a value of zero. The decision to
                 skip non-covered regions depends on the interpretation
                 of the data. Non-covered regions may represent, for
                 example, repetitive regions that should be ignored.
                 (default: False)" />
    </xml>

    <xml name="input_save_matrix_values">
        <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>