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view gmql_operators_select.xml @ 0:a80c93182db3 draft default tip
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
author | geco-team |
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date | Tue, 26 Jun 2018 09:08:06 -0400 |
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<macros> <import>gmql_queries_macros.xml</import> <xml name="select"> <conditional name="input"> <param name="input_type" type="select" display="radio" label="Dataset over which SELECT samples" help="It can be a dataset in the user space or the result of a MATERIALIZE operation still to be executed."> <option value="i_ds">User Dataset</option> <option value="i_var">Materializing result</option> </param> <when value="i_ds"> <param name="gmql_datasets" type="data" format="gmql_repository" label="Working Datasets" /> <param name="input_ds" type="select" label="Select Dataset" refresh_on_change="True"> <options from_dataset="gmql_datasets"> <column name="value" index="0"/> </options> </param> <expand macro="predicates"> <expand macro="advanced_mode"> <expand macro="meta_block" optional="true" vartype="select"/> <repeat name="add_meta_blocks" title="Additional Conditions Block" default="0" min="0" help="Compose different blocks to obtain more complex conditions"> <expand macro="meta_block" vartype="select"> <expand macro="block_logCon"/> </expand> </repeat> </expand> </expand> </when> <when value="i_var"> <expand macro="input_var" name="input_var" label="Variable name" optional="false"/> <expand macro="predicates"> <expand macro="advanced_mode"> <expand macro="meta_block" optional="true" vartype="text"/> <repeat name="add_meta_blocks" title="Additional Conditions Block" default="0" min="0" help="Compose different blocks to obtain more complex conditions"> <expand macro="meta_block" vartype="text"> <expand macro="block_logCon"/> </expand> </repeat> </expand> </expand> </when> </conditional> <expand macro="output_var" /> <expand macro="materialize_stm" /> </xml> <xml name="predicates"> <section name="metadata_predicates" title="Conditions on metadata" expanded="false" help="Selection based on the existence and values of certain metadata attributes in each sample."> <yield/> </section> <section name="region_predicates" title="Conditions on region fields" expanded="false" help="Selection based on the characteristics of the genomic regions of each sample."> <expand macro="advanced_mode"> <expand macro="region_block" optional="true"/> <repeat name="add_region_blocks" title="Additional Conditions Block" default="0" min="0" help="Compose different blocks to obtain more complex conditions"> <expand macro="region_block"> <expand macro="block_logCon"/> </expand> </repeat> </expand> </section> <section name="semijoin_predicate" title="Conditions in relation of an external datasets" expanded="false" help="Selection based on the existence of certain metadata attributes and the matching of their values with those associated with at least one sample in an external dataset D_EXT"> <expand macro="semijoin"/> </section> </xml> <xml name="advanced_mode"> <conditional name="conditions"> <param name="ad_flag" type="select" display="radio" label="Build up conditions step by step or use advance mode to directly type the logical formula."> <option value="steps">Step by step</option> <option value="string">Advanced mode</option> </param> <when value="string"> <param name="conditions_string" type="text" label="Conditions" area="true" help="For details on the format check the GMQL Manual" /> </when> <when value="steps"> <yield /> </when> </conditional> </xml> <xml name="meta_block" token_optional="optional" token_vartype="vartype"> <yield /> <expand macro="metadata_predicate" optional="@OPTIONAL@" vartype="@VARTYPE@"/> <repeat name="pm_additional" title="Additional Condition" min="0" default="0"> <expand macro="metadata_predicate" vartype="@VARTYPE@"> <expand macro="logCon"/> </expand> </repeat> </xml> <xml name="metadata_predicate" token_optional="optional" token_vartype="vartype"> <yield /> <param name="negate" type="boolean" label="Negative Condition" optional="@OPTIONAL@"/> <param name="attribute" type="@VARTYPE@" label="Metadata Attribute Name" optional="@OPTIONAL@" refresh_on_change="True" dynamic_options="get_metadata_attr(user=authToken.file_name,ds=input_ds, ds_list=gmql_datasets.file_name)" /> <expand macro="condition" optional="@OPTIONAL@" /> <param name="value" type="select" label="Value whom to confront the metadata attribute with" optional="@OPTIONAL@" dynamic_options="get_metadata_values(user=authToken.file_name, ds=input_ds, ds_list=gmql_datasets.file_name, att=attribute)" /> </xml> <xml name="region_block" token_optional="optional"> <yield /> <expand macro="region_predicate" optional="@OPTIONAL@"/> <repeat name="pr_additional" title="Additional Condition" min="0" default="0"> <expand macro="region_predicate"> <expand macro="logCon"/> </expand> </repeat> </xml> <xml name="region_predicate" token_optional="optional"> <yield /> <param name="negate" type="boolean" label="Negative Condition" optional="@OPTIONAL@" /> <param name="attribute" type="text" label="Region Attribute Name" optional="@OPTIONAL@" > <expand macro="region_attribute" /> </param> <expand macro="condition" optional="@OPTIONAL@" /> <param name="value" type="text" label="Value whom to confront the region attribute with" optional="@OPTIONAL@" > <expand macro="region_value"/> </param> <param name="is_meta_value" type="boolean" label="Is it the confront value a metadata field?" optional="@OPTIONAL@" help="The use of metadata attributes in predicates on region attributes is enabled." /> </xml> <xml name="semijoin"> <repeat name="sj_attributes" title="Metadata Attributes to match in DS_EXT" min="0" default="0"> <expand macro="metajoin_attribute" name="sj_att" /> </repeat> <param name="condition" type="select" label="Condition"> <option value="IN">IN</option> <option value="NOT_IN">NOT IN</option> </param> <expand macro="input_var" name="ds_ext" label="DS_EXT" optional="true" /> </xml> <xml name="region_attribute"> <expand macro="text_val" /> <option value="chr">chr</option> <option value="left">left</option> <option value="right">right</option> <option value="strand">strand</option> <option value="region_field">region_field</option> </xml> <xml name="region_value"> <validator type="regex" message="Valid characters are letters, digits, '.', +, -, and the wildcard symbol '*'">[+\-\*]|([\d]+\.)?[\d]+|[\w]+$</validator> <option value="*">any value</option> <option value="string">string</option> <option value="1">1</option> <option value="0.0">0.0</option> <option value="+">+</option> <option value="-">-</option> </xml> <xml name="condition" token_optional="optional"> <param name="condition" type="select" label="Condition" optional="@OPTIONAL@"> <option value="eq"><![CDATA[ == ]]></option> <option value="gt"><![CDATA[ > ]]></option> <option value="lt"><![CDATA[ < ]]></option> <option value="get"><![CDATA[ >= ]]></option> <option value="let"><![CDATA[ <= ]]></option> </param> </xml> </macros>