Mercurial > repos > geco-team > gmql_queries_composer
diff 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 |
|---|---|
| date | Tue, 26 Jun 2018 09:08:06 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gmql_operators_select.xml Tue Jun 26 09:08:06 2018 -0400 @@ -0,0 +1,167 @@ +<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> \ No newline at end of file