annotate gmql_operators_project.xml @ 0:a80c93182db3 draft default tip

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

<macro>
    <import>gmql_queries_macros.xml</import>
    <xml name="project">
        <expand macro="input_var" name="input_var" label="Input Dataset" />
        <expand macro="output_var" />
        <expand macro="sec_attributes" sec="region_att" title="Region attributes to keep" attname="Region Attribute"/>
        <expand macro="sec_attributes" sec="meta_att" title="Metadata attributes to keep" attname="Metadata Attribute"/>
        <section name="project_new_regions" title="New Genomic Region Attributes" expanded="false"
                 help="Generate new genomic region attributes functions on existing region or metadata attributes or
                 constants. It is also possible to rename an existing field." >
            <repeat name="new_region_att" title="Define Region Attribute" min="0">
                <param name="new_name" type="text" label="New attribute name">
                    <expand macro="text_val"/>
                </param>
                <conditional name="gen_function">
                    <expand macro="gen_type_functions" label="Type of function to apply to generate new region attribute">
                        <option value="NULL">Define a new numeric region attribute with "null" value</option>
                        <option value="META">Value of a metadata attribute</option>
                    </expand>
                    <expand macro="gen_arguments">
                        <when value="NULL">
                            <param name="att_type" type="select" label="Type of new attribute">
                                <option value="INTEGER">INTEGER</option>
                                <option value="INTEGER">DOUBLE</option>
                            </param>
                        </when>
                        <when value="META">
                            <expand macro="f_argument" label="Name of the metadata attribute to use as source"/>
                            <param name="att_type" type="select" label="Type of new attribute">
                                <option value="INTEGER">INTEGER</option>
                                <option value="INTEGER">DOUBLE</option>
                                <option value="STRING">STRING (for any case when the attribute has not numerical values)</option>
                            </param>
                        </when>
                    </expand>
                </conditional>
            </repeat>
        </section>
        <section name="project_new_meta" title="New Metadata Attributes" expanded="false"
                 help="Generate new metadata attributes functions on existing metadata attributes or constants.
                 It is also possible to rename an existing field." >
                <repeat name="new_meta_att" title="Define Metadata Attribute" min="0">
                    <param name="new_name" type="text" label="New attribute name" >
                        <expand macro="text_val" />
                    </param>
                    <conditional name="gen_function">
                        <expand macro="gen_type_functions" label="Type of function to apply to generate new metadata attribute">
                        </expand>
                        <expand macro="gen_arguments" >
                        </expand>
                    </conditional>
                </repeat>
        </section>
        <expand macro="materialize_stm" />
    </xml>
    <xml name="gen_type_functions" token_label="@LABEL@">
        <param name="gen_type" type="select" label="@LABEL@">
            <option value="aggregate">Aggregate function</option>
            <option value="arithmetic">Arithmetic expression</option>
            <option value="SQRT">Square root</option>
            <option value="rename">Rename a field</option>
            <option value="fixed">Create and set all instances to a value</option>
            <yield />
        </param>
    </xml>
    <xml name="gen_arguments">
        <when value="aggregate">
            <expand macro="aggrFuncs" optional="true"
                    help="Sum, average, maximum, minimum and standard deviation are only for numerical attributes"
                    label="Function to apply to generate new region attribute"/>
            <expand macro="f_argument" label="Region attribute over which apply function"/>
        </when>
        <when value="arithmetic">
            <param name="expression" label="Expression" type="text"
                   help="All basic mathematical operations (+, -, *, /), including usage of parenthesis">
                <validator type="regex" message="It includes not valid characters">[\w\.\(\)\-\+\*\/\s]+</validator>
            </param>
        </when>
        <when value="SQRT">
            <expand macro="f_argument" label="Region attribute over which apply function"/>
        </when>
        <when value="rename">
            <expand macro="f_argument" label="New name"/>
        </when>
        <when value="fixed">
            <expand macro="f_argument" label="Defined value"/>
        </when>
        <yield/>
    </xml>
    <xml name="f_argument" token_label="@LABEL@">
        <param name="arg" type="text" label="@LABEL@">
            <expand macro="text_val"/>
        </param>
    </xml>
    <xml name="sec_attributes" token_sec="@SEC@" token_title="@TITLE@" token_attname="@ATTNAME@">
        <section name="@SEC@" title="@TITLE@"
                 help="The PROJECT operator creates, from an existing dataset, a new dataset with all the samples
        (with their regions and region values) in the input one, but keeping for each sample in the input dataset
        only those metadata and/or region attributes expressed in the following sections. Note that if no
        options are given, the default behavior is to remove all the region attributes which are not coordinates
        (i.e., only chr, start, stop, and strand are kept)">
            <conditional name="allbut">
                <param name="allbut_flag" type="select" label="How to list attributes">
                    <option value="keep">List only the ones to keep</option>
                    <option value="exclude">Keep all attributes and list what to exclude</option>
                </param>
                <when value="keep">
                    <expand macro="attribute_field" name="list_keep" min="1" attname="@ATTNAME@" />
                </when>
                <when value="exclude">
                    <expand macro="attribute_field" name="list_exclude" min="0" attname="@ATTNAME@" />
                </when>
            </conditional>
        </section>
    </xml>
    <xml name="attribute_field" token_name="@NAME@" token_min="@MIN@" token_attname="@ATTNAME@">
       <repeat name="@NAME@" min="@MIN@" title="@ATTNAME@"
                            help="The wildcard '?' can be used in place of the syntax (at most one per attribute)">
           <param name="attribute" type="text" label="Attribute Name" optional="true">
                <validator type="regex" message="Format not valid">(\?\.)?[\w]+|[\w]+(\.\?)|(\?\.)[\w]+(\.\?)$</validator>
                <option value="attribute">attribute</option>
                <option value="?.attribute">?.attribute</option>
                <option value="dataset.?">dataset.?</option>
                <option value="dataset.?.attribute">dataset.?.attribute</option>
            </param>
       </repeat>
    </xml>
</macro>