annotate gmql_operators_group.xml @ 0:a80c93182db3 draft default tip

planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty

<macros>
    <import>gmql_queries_macros.xml</import>
    <xml name="group">
        <expand macro="input_var" name="input_var" label="Input Dataset" optional="false" />
        <expand macro="output_var" />
        <conditional name="add_grouping">
            <param name="group_type" type="select" label="Additional Grouping Options"
                   help="If the defualt option is set, it will group only on the region attributes which represent
                   the four genomic coordinates (chr, start, stop, and strand). Inside a single sample, it collapses
                   all regions that have equal values in these four coordinates into a single one, thus eliminating duplicate regions" >
                <option value="default">Only default attributes (genomic coordinates)</option>
                <option value="meta">Group also on metadata attributes</option>
                <option value="regions">Group also on other region attributes and/or create new region fields with aggregate functions</option>
                <option value="both">Group also on both metadata and other regions attributes</option>
            </param>
            <when value="default">
                <!-- do nothing -->
            </when>
            <when value="meta">
                <expand macro="metadata_options" />
            </when>
            <when value="regions">
                <expand macro="region_options" />
            </when>
            <when value="both">
                <expand macro="metadata_options" />
                <expand macro="region_options" />
            </when>
        </conditional>
        <expand macro="materialize_stm" />
    </xml>
    <xml name="region_options">
        <section name="regions" title="Additional grouping options over region attributes" expanded="true"
                 help="In each sample, regions found in the same group (i.e., regions with same coordinates and
                 grouping attribute values), are combined into a single region; this allows to merge regions that are
                 duplicated inside the same sample (based on the values of their coordinates and of other possible
                 specified region attributes)">
            <repeat name="group_regions_atts" min="0" title="Grouping Region Attribute">
                <param name="attribute" type="text" label="Region Attribute">
                    <expand macro="text_val" />
                    <validator type="expression" message="Coordinate attributes are already used by default">value not in ['chr','left','right','strand']</validator>
                </param>
            </repeat>
            <expand macro="att_generator" title="Aggregate Region Attribute" min="0"/>
        </section>
    </xml>
    <xml name="metadata_options">
        <section name="metadata" title="Grouping Options over metadata attributes" expanded="true"
                 help="GROUP performs the grouping of samples of the input dataset based on one specified metadata
                    attribute. If the metadata attribute is multi-value, the grouping identifies different groups of
                    samples for each attribute value combination. All metadata in the input samples are conserved,
                    with the addition of the _group attribute, whose value is the identifier of the group to which
                    the specific sample is assigned. Samples having missing values for any of the grouping metadata
                    attributes are assigned all together to one group, identified by the special value _group = 0">
            <repeat name="group_meta_atts" min="1" title="Grouping Metadata Attribute">
                <expand macro="metajoin_attribute" name="j_att" optional="true" >
                <expand macro="metajoin_options" />
            </expand>
            </repeat>
            <conditional name="meta_agg">
                <param name="meta_agg_flag" type="boolean" label="Create new aggregate attributes?"
                       help="It is possible to request the evaluation of aggregate functions on metadata attributes;
                       these functions consider the metadata contained in all samples of each group" />
                <when value="true">
                    <expand macro="att_generator" title="Aggregate Metadata Attribute" min="1" />
                </when>
            </conditional>
        </section>
    </xml>
    <xml name="att_generator" token_title="@TITLE@" token_min="@MIN@">
        <repeat name="new_attributes" title="@TITLE@" min="@MIN@">
            <param name="new_name" type="text" label="New Attribute Name">
                <expand macro="text_val"/>
            </param>
            <expand macro="aggrFuncs" help="Sum, average, maximum, minimum and standard deviation are only for numerical
                attributes" optional="false" label="Aggregate Function to apply" />
            <param name="argument" label="Attributes over which apply function" type="text">
                <expand macro="text_val"/>
            </param>
        </repeat>
    </xml>
</macros>