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view gmql_operators_tests.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> <xml name="query_intro" token_name="@NAME@"> <param name="authToken" value="guest2.gmql_user"/> <param name="query_name" value="@NAME@"/> <conditional name="query_create"> <param name="create" value="yes"/> </conditional> </xml> <xml name="query_end" token_mat="@MAT@"> <conditional name="materialize"> <param name="materialize_result" value="@MAT@"/> <yield /> </conditional> </xml> <xml name="simple_select" token_ds="@DS@"> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="SELECT"/> <conditional name="input"> <param name="input_type" value="i_ds"/> <param name="gmql_datasets" value="rep.gmql_repository"/> <param name="input_ds" value="@DS@"/> <section name="region_predicates"> <conditional name="conditions"> <param name="ad_flags" value="strings"/> <param name="conditions_string" value=""/> </conditional> </section> <section name="metadata_predicates"> <conditional name="conditions"> <param name="ad_flags" value="strings"/> <param name="conditions_string" value=""/> </conditional> </section> <section name="semijoin_predicate"> <param name="condition" value="IN"/> <param name="ds_ext" value=""/> </section> </conditional> <yield /> </conditional> </repeat> </xml> <xml name="composer_tests"> <tests> <test> <!-- TEST 1: Select (Simple Metadata Condition) --> <expand macro="query_intro" name="test_select1"/> <repeat name="operations"> <conditional name="operation" > <param name="operator" value="SELECT"/> <conditional name="input"> <param name="input_type" value="i_ds"/> <param name="gmql_datasets" value="rep.gmql_repository"/> <param name="input_ds" value="Example_Dataset_1"/> <section name="metadata_predicates"> <conditional name="conditions"> <param name="ad_flags" value="steps"/> <param name="negate" value="false"/> <param name="attribute" value="grant"/> <param name="condition" value="eq"/> <param name="value" value="Stam"/> </conditional> </section> <section name="region_predicates"> <conditional name="conditions"> <param name="ad_flags" value="strings"/> <param name="conditions_string" value=""/> </conditional> </section> <section name="semijoin_predicate"> <param name="condition" value="IN"/> <param name="ds_ext" value=""/> </section> </conditional> </conditional> </repeat> <param name="output_var" value="OUT"/> <conditional name="m_stm"> <param name="materialize_stm" value="false" /> </conditional> <expand macro="query_end" mat="false"/> <output name="query" file="select1.gmql_query"/> </test> <test> <!-- TEST 2: Select (Multiple Metadata, Region condition) --> <expand macro="query_intro" name="test_select2"/> <repeat name="operations"> <conditional name="operation" > <param name="operator" value="SELECT"/> <conditional name="input"> <param name="input_type" value="i_ds"/> <param name="gmql_datasets" value="rep.gmql_repository"/> <param name="input_ds" value="Example_Dataset_1" /> <section name="region_predicates"> <conditional name="conditions"> <param name="is_meta_value" value="false" /> <param name="ad_flag" value="steps" /> <param name="attribute" value="score" /> <param name="value" value="3" /> <param name="negate" value="false" /> <param name="condition" value="gt" /> </conditional> </section> <section name="metadata_predicates" > <conditional name="conditions" > <param name="ad_flag" value="steps" /> <param name="attribute" value="patient_age" /> <param name="value" value="64" /> <param name="negate" value="false" /> <param name="condition" value="eq" /> <repeat name="pm_additional" > <param name="negate" value="false" /> <param name="attribute" value="cell" /> <param name="logCon" value="AND" /> <param name="value" value="8988T" /> <param name="condition" value="eq" /> </repeat> </conditional> </section> <section name="semijoin_predicate"> <param name="condition" value="IN"/> <param name="ds_ext" value=""/> </section> </conditional> </conditional> </repeat> <param name="output_var" value="OUT"/> <conditional name="m_stm"> <param name="materialize_stm" value="false" /> </conditional> <expand macro="query_end" mat="false"/> <output name="query" file="select2.gmql_query"/> </test> <test> <!-- TEST 3: Select (TEST2 + Semijoin predicate) --> <expand macro="query_intro" name="test_select3"/> <repeat name="operations"> <conditional name="operation" > <param name="operator" value="SELECT"/> <conditional name="input"> <param name="input_type" value="i_ds"/> <param name="gmql_datasets" value="rep.gmql_repository"/> <param name="input_ds" value="Example_Dataset_1" /> <section name="region_predicates"> <conditional name="conditions"> <param name="is_meta_value" value="false" /> <param name="ad_flag" value="steps" /> <param name="attribute" value="score" /> <param name="value" value="3" /> <param name="negate" value="false" /> <param name="condition" value="gt" /> </conditional> </section> <section name="metadata_predicates" > <conditional name="conditions" > <param name="ad_flag" value="steps" /> <param name="attribute" value="patient_age" /> <param name="value" value="64" /> <param name="negate" value="false" /> <param name="condition" value="eq" /> <repeat name="pm_additional" > <param name="negate" value="false" /> <param name="attribute" value="cell" /> <param name="logCon" value="AND" /> <param name="value" value="8988T" /> <param name="condition" value="eq" /> </repeat> </conditional> </section> <section name="semijoin_predicate"> <param name="condition" value="IN"/> <param name="ds_ext" value=""/> </section> </conditional> </conditional> </repeat> <param name="output_var" value="OUT"/> <conditional name="m_stm"> <param name="materialize_stm" value="false" /> </conditional> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="SELECT" /> <conditional name="input"> <param name="input_type" value="i_ds"/> <param name="gmql_datasets" value="rep.gmql_repository"/> <param name="input_ds" value="Example_Dataset_2" /> <section name="region_predicates"> <conditional name="conditions"> <param name="ad_flags" value="strings"/> <param name="conditions_string" value=""/> </conditional> </section> <section name="metadata_predicates"> <conditional name="conditions"> <param name="ad_flags" value="strings"/> <param name="conditions_string" value=""/> </conditional> </section> <section name="semijoin_predicate"> <repeat name="sj_attributes" > <param name="sj_att" value="cell" /> </repeat> <param name="ds_ext" value="OUT" /> </section> </conditional> <param name="output_var" value="OUT2"/> </conditional> </repeat> <expand macro="query_end" mat="false"/> <output name="query" file="select3.gmql_query"/> </test> <test> <!-- TEST 4: PROJECT --> <expand macro="query_intro" name="test_project1"/> <expand macro="simple_select" ds="Example_Dataset_1" /> <param name="output_var" value="OUT"/> <conditional name="m_stm"> <param name="materialize_stm" value="false" /> </conditional> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="PROJECT"/> <param name="input_var" value="OUT"/> <section name="region_att"> <conditional name="allbut"> <param name="allbut_flag" value="exclude"/> <repeat name="list_exclude"> <param name="attribute" value="name"/> </repeat> <repeat name="list_exclude"> <param name="attribute" value="frame"/> </repeat> </conditional> </section> <section name="meta_att"> <conditional name="allbut"> <param name="allbut_flag" value="keep"/> <repeat name="list_keep"> <param name="attribute" value="cell"/> </repeat> </conditional> </section> <section name="project_new_meta"/> <section name="project_new_regions"> <repeat name="new_region_att"> <param name="new_name" value="lengh"/> <conditional name="gen_function"> <param name="expression" value="stop - start"/> <param name="gen_type" value="arithmetic"/> </conditional> </repeat> </section> <param name="output_var" value="OUT2"/> </conditional> </repeat> <output name="query" file="project1.gmql_query"/> </test> <test> <!-- TEST 5: EXTEND --> <expand macro="query_intro" name="test_extend1"/> <expand macro="simple_select" ds="Example_Dataset_1"/> <param name="output_var" value="OUT"/> <conditional name="m_stm"> <param name="materialize_stm" value="false"/> </conditional> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="EXTEND"/> <section name="new_metadata_attributes"> <repeat name="new_attributes"> <param name="new_name" value="avg_score"/> <param name="function" value="AVG"/> <param name="argument" value="score"/> </repeat> <repeat name="new_attributes"> <param name="new_name" value="max_p"/> <param name="function" value="MAX"/> <param name="argument" value="pvalue"/> </repeat> </section> <param name="input_var" value="OUT" /> <param name="output_var" value="OUT2"/> </conditional> </repeat> <output name="query" file="extend1.gmql_query" /> </test> <test> <!-- TEST 6: ORDER --> <expand macro="query_intro" name="test_order1" /> <expand macro="simple_select" ds="Example_Dataset_1" /> <param name="output_var" value="OUT" /> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="ORDER"/> <param name="output_var" value="OUT2"/> <param name="input_var_ordering_ds" value="OUT"/> <section name="ordering_attributes"> <repeat name="attributes"> <param name="attribute_name" value="score"/> <param name="att_type" value="region"/> <param name="order_type" value="desc"/> </repeat> <repeat name="attributes"> <param name="attribute_name" value="start"/> <param name="att_type" value="region"/> <param name="order_type" value="asc"/> </repeat> <repeat name="attributes"> <param name="attribute_name" value="ID"/> <param name="att_type" value="metadata"/> <param name="order_type" value="asc"/> </repeat> </section> <section name="top_options"> <repeat name="to"> <param name="type" value="metadata"/> <conditional name="opt"> <param name="k_type" value="n"/> <param name="k" value="5"/> </conditional> </repeat> </section> </conditional> </repeat> <output name="query" file="order1.gmql_query" /> </test> <test> <!-- TEST 7: GROUP --> <expand macro="query_intro" name="test_group1"/> <expand macro="simple_select" ds="Example_Dataset_1"/> <param name="output_var" value="OUT"/> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="GROUP"/> <param name="output_var" value="OUT2"/> <param name="input_var" value="OUT"/> <conditional name="add_grouping"> <param name="group_type" value="both"/> <section name="regions"> <repeat name="group_regions_atts"> <param name="attribute" value="score"/> </repeat> <repeat name="new_attributes"> <param name="new_name" value="min_signal"/> <param name="function" value="MIN"/> <param name="argument" value="signal"/> </repeat> </section> <section name="metadata"> <conditional name="meta_agg"> <param name="meta_agg_flag" value="true"/> <repeat name="new_attributes"> <param name="new_name" value="min_tier"/> <param name="function" value="MIN"/> <param name="argument" value="cell_tier"/> </repeat> </conditional> <repeat name="group_meta_atts"> <param name="metajoin_match" value="SIMPLE"/> <param name="j_att" value="cell_tissue"/> </repeat> </section> </conditional> </conditional> </repeat> <output name="query" file="group1.gmql_query" /> </test> <test> <!-- TEST 8: MERGE --> <expand macro="query_intro" name="test_merge1"/> <expand macro="simple_select" ds="Example_Dataset_1"/> <param name="output_var" value="OUT"/> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="MERGE"/> <param name="output_var" value="OUT2"/> <param name="input_var" value="OUT"/> <section name="groupby"> <repeat name="group_meta_atts"> <param name="metajoin_match" value="EXACT"/> <param name="j_att" value="antibody_target"/> </repeat> </section> </conditional> </repeat> </test> <test> <!-- TEST 9: UNION --> <expand macro="query_intro" name="test_merge1"/> <expand macro="simple_select" ds="Example_Dataset_1"/> <param name="output_var" value="IN"/> <expand macro="simple_select" ds="Example_Dataset_2" > <param name="output_var" value="IN2" /> </expand> <repeat name="operations"> <conditional name="operation" > <param name="operator" value="UNION" /> <param name="output_var" value="OUT" /> <param name="input_var_second" value="IN2" /> <param name="input_var_first" value="IN" /> </conditional> </repeat> <output name="query" file="union1.gmql_query" /> </test> <test> <!-- TEST 10: DIFFERENCE --> <expand macro="query_intro" name="test_merge1"/> <expand macro="simple_select" ds="Example_Dataset_1"/> <param name="output_var" value="IN"/> <expand macro="simple_select" ds="Example_Dataset_2"> <param name="output_var" value="IN2"/> </expand> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="DIFFERENCE"/> <param name="output_var" value="OUT"/> <param name="input_var_negative" value="IN2"/> <param name="input_var_reference" value="IN"/> <param name="exact_flag" value="true"/> <section name="joinby"> <repeat name="group_meta_atts"> <param name="metajoin_match" value="SIMPLE"/> <param name="j_att" value="cell"/> </repeat> </section> </conditional> </repeat> <output name="query" file="difference1.gmql_query"/> </test> <test> <!-- TEST 11: JOIN (Genomic Predicate + Joinby condition) --> <expand macro="query_intro" name="test_join1"/> <expand macro="simple_select" ds="Example_Dataset_1"/> <param name="output_var" value="IN"/> <expand macro="simple_select" ds="Example_Dataset_2"> <param name="output_var" value="IN2"/> </expand> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="JOIN"/> <param name="output_var" value="OUT"/> <param name="input_var_anchor" value="IN"/> <param name="input_var_experiment" value="IN2"/> <section name="conditions_section"> <conditional name="conditions"> <param name="c_type" value="distance"/> <repeat name="distance_conditions"> <conditional name="type_dc"> <param name="type_dc_value" value="dist"/> <param name="dc" value="MD"/> <param name="n" value="1"/> </conditional> </repeat> <repeat name="distance_conditions"> <conditional name="type_dc"> <param name="type_dc_value" value="stream"/> <param name="ds" value="UP"/> </conditional> </repeat> <param name="output_opt" value="RIGHT"/> </conditional> </section> <section name="joinby"> <repeat name="joinby_clause"> <param name="metajoin_match" value="SIMPLE"/> <param name="j_att" value="cell"/> </repeat> </section> </conditional> </repeat> <output name="query" file="join1.gmql_query"/> </test> <test> <!-- TEST 12: JOIN (Genomic Predicate, Region Conditions, Joinby) --> <expand macro="query_intro" name="test_join2"/> <expand macro="simple_select" ds="Example_Dataset_1"/> <param name="output_var" value="IN"/> <expand macro="simple_select" ds="Example_Dataset_2"> <param name="output_var" value="IN2"/> </expand> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="JOIN"/> <param name="input_var_anchor" value="IN"/> <param name="output_var" value="OUT"/> <param name="input_var_experiment" value="IN2"/> <section name="conditions_section"> <conditional name="conditions"> <param name="c_type" value="both"/> <repeat name="distance_conditions"> <conditional name="type_dc"> <param name="type_dc_value" value="dist"/> <param name="dc" value="DL"/> <param name="n" value="0"/> </conditional> </repeat> <param name="output_opt" value="INT"/> <repeat name="region_attributes"> <param name="attribute" value="score" /> </repeat> <repeat name="region_attributes"> <param name="attribute" value="chr" /> </repeat> </conditional> </section> <section name="joinby"> <repeat name="joinby_clause"> <param name="metajoin_match" value="SIMPLE"/> <param name="j_att" value="cell"/> </repeat> <repeat name="joinby_clause"> <param name="metajoin_match" value="SIMPLE"/> <param name="j_att" value="provider"/> </repeat> </section> </conditional> </repeat> <output name="query" file="join2.gmql_query"/> </test> <test> <!-- TEST 13: MAP --> <expand macro="query_intro" name="test_map1"/> <expand macro="simple_select" ds="Example_Dataset_1"/> <param name="output_var" value="IN"/> <expand macro="simple_select" ds="Example_Dataset_2"> <param name="output_var" value="IN2"/> </expand> <repeat name="operations"> <conditional name="operation"> <param name="input_var_reference" value="IN"/> <param name="output_var" value="OUT"/> <param name="count_result" value="mapped_n"/> <param name="input_var_experiment" value="IN2"/> <param name="operator" value="MAP"/> <section name="new_regions_attributes"> <repeat name="new_regions"> <param name="new_name" value="avg_score"/> <param name="function" value="AVG"/> <param name="argument" value="score"/> </repeat> <repeat name="new_regions"> <param name="new_name" value="min_score"/> <param name="function" value="MIN"/> <param name="argument" value="score"/> </repeat> <repeat name="new_regions"> <param name="new_name" value="chr_list"/> <param name="function" value="BAG"/> <param name="argument" value="chr"/> </repeat> </section> <section name="joinby"> <repeat name="joinby_clause"> <param name="metajoin_match" value="SIMPLE"/> <param name="j_att" value="cell_tissue"/> </repeat> </section> </conditional> </repeat> <output name="query" file="map1.gmql_query"/> </test> <test> <!-- TEST 13: COVER (Base Variant) --> <expand macro="query_intro" name="test_cover1"/> <expand macro="simple_select" ds="Example_Dataset_1"/> <param name="output_var" value="IN"/> <repeat name="operations"> <conditional name="operation"> <param name="output_var" value="OUT"/> <param name="cover_variant" value="COVER"/> <param name="input_var" value="IN"/> <param name="operator" value="COVER"/> <conditional name="minAcc"> <param name="min_type" value="value"/> <param name="value" value="1"/> </conditional> <conditional name="maxAcc"> <param name="max_type" value="ANY"/> </conditional> <section name="new_regions_attributes"> <repeat name="new_regions"> <param name="new_name" value="min_pvalue"/> <param name="function" value="MIN"/> <param name="argument" value="pvalue"/> </repeat> </section> <section name="groupby"> <repeat name="groupby_clause"> <param name="metajoin_match" value="SIMPLE"/> <param name="j_att" value="cell"/> </repeat> <repeat name="groupby_clause"> <param name="metajoin_match" value="SIMPLE"/> <param name="j_att" value="antibody_target"/> </repeat> </section> </conditional> </repeat> <output name="query" file="cover1.gmql_query"/> </test> <test> <!-- TEST 14: COVER (Variants) --> <expand macro="query_intro" name="test_cover2"/> <expand macro="simple_select" ds="Example_Dataset_1"/> <param name="output_var" value="IN"/> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="COVER"/> <param name="output_var" value="OUT1"/> <param name="cover_variant" value="FLAT"/> <param name="input_var" value="IN"/> <conditional name="minAcc"> <param name="min_type" value="value"/> <param name="value" value="2"/> </conditional> <conditional name="maxAcc"> <param name="max_type" value="value"/> <param name="value" value="4"/> </conditional> <section name="groupby"> <repeat name="groupby_clause"> <param name="metajoin_match" value="SIMPLE"/> <param name="j_att" value="cell"/> </repeat> </section> </conditional> </repeat> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="COVER"/> <param name="output_var" value="OUT2"/> <param name="cover_variant" value="SUMMIT"/> <param name="input_var" value="IN"/> <conditional name="minAcc"> <param name="min_type" value="value"/> <param name="value" value="2"/> </conditional> <conditional name="maxAcc"> <param name="max_type" value="value"/> <param name="value" value="4"/> </conditional> <section name="groupby"> <repeat name="groupby_clause"> <param name="metajoin_match" value="SIMPLE"/> <param name="j_att" value="cell"/> </repeat> </section> </conditional> </repeat> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="COVER"/> <param name="output_var" value="OUT3"/> <param name="cover_variant" value="HISTOGRAM"/> <param name="input_var" value="IN"/> <conditional name="minAcc"> <param name="min_type" value="ALL_n"/> <param name="n" value="2"/> </conditional> <conditional name="maxAcc"> <param name="max_type" value="ALL_n_k"/> <param name="k" value="1"/> <param name="n" value="2"/> </conditional> <section name="groupby"> <repeat name="groupby_clause"> <param name="metajoin_match" value="SIMPLE"/> <param name="j_att" value="antibody_target"/> </repeat> </section> </conditional> </repeat> <output name="query" file="cover2.gmql_query"/> </test> <test> <!-- TEST 15: Query Compilation --> <expand macro="query_intro" name="test_compile"/> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="SELECT"/> <conditional name="input"> <param name="input_type" value="i_ds"/> <param name="gmql_datasets" value="rep.gmql_repository"/> <param name="input_ds" value="Example_Dataset_1"/> <section name="metadata_predicates"> <conditional name="conditions"> <param name="ad_flags" value="steps"/> <param name="negate" value="false"/> <param name="attribute" value="grant"/> <param name="condition" value="eq"/> <param name="value" value="Stam"/> </conditional> </section> <section name="region_predicates"> <conditional name="conditions"> <param name="ad_flags" value="strings"/> <param name="conditions_string" value=""/> </conditional> </section> <section name="semijoin_predicate"> <param name="condition" value="IN"/> <param name="ds_ext" value=""/> </section> </conditional> </conditional> </repeat> <param name="output_var" value="VAR"/> <conditional name="materialize"> <param name="file_name" value="TG"/> <param name="materialize_result" value="true"/> <conditional name="choose_op"> <param name="op" value="compile"/> </conditional> </conditional> <output name="query" file="query.gmql_query"/> <output name="log" ftype="txt"> <assert_contents> <has_text text="COMPILE_SUCCESS"/> </assert_contents> </output> </test> <test> <!-- TEST 16: Query Execution --> <param name="authToken" value="guest2.gmql_user"/> <param name="query_name" value="testexec"/> <conditional name="query_create"> <param name="create" value="yes"/> </conditional> <repeat name="operations"> <conditional name="operation"> <param name="operator" value="SELECT"/> <conditional name="input"> <param name="input_type" value="i_ds"/> <param name="gmql_datasets" value="rep.gmql_repository"/> <param name="input_ds" value="Example_Dataset_1"/> <section name="metadata_predicates"> <conditional name="conditions"> <param name="ad_flags" value="steps"/> <param name="negate" value="false"/> <param name="attribute" value="grant"/> <param name="condition" value="eq"/> <param name="value" value="Stam"/> </conditional> </section> <section name="region_predicates"> <conditional name="conditions"> <param name="ad_flags" value="strings"/> <param name="conditions_string" value=""/> </conditional> </section> <section name="semijoin_predicate"> <param name="condition" value="IN"/> <param name="ds_ext" value=""/> </section> </conditional> </conditional> </repeat> <param name="output_var" value="VAR"/> <conditional name="materialize"> <param name="file_name" value="TG"/> <param name="materialize_result" value="true"/> <conditional name="choose_op"> <param name="op" value="run"/> <param name="out_format" value="gdm"/> <param name="import" value="true"/> </conditional> </conditional> <output name="query" file="query.gmql_query"/> <output name="log" ftype="txt"> <assert_contents> <has_text text="SUCCESS"/> </assert_contents> </output> <output name="updated_list" ftype="gmql_repository"> <assert_contents> <has_text_matching expression="testexec_\d+_\d+_TG"/> </assert_contents> </output> <collection name="query_results_s" type="list"> <metadata name="name" value="testexec results"/> <discovered_dataset designation="S00000" file="TG/S_00000.gdm"/> <discovered_dataset designation="S00001" file="TG/S_00001.gdm"/> <discovered_dataset designation="S00002" file="TG/S_00002.gdm"/> </collection> <collection name="query_results_m" type="list"> <metadata name="name" value="testexec results metadata"/> <discovered_dataset designation="S00000" file="TG/S_00000.gdm.meta"/> <discovered_dataset designation="S00001" file="TG/S_00001.gdm.meta"/> <discovered_dataset designation="S00002" file="TG/S_00002.gdm.meta"/> </collection> </test> </tests> </xml> </macros>