Mercurial > repos > iuc > query_tabular
diff query_tabular.xml @ 4:973f03d82c86 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
| author | iuc |
|---|---|
| date | Thu, 03 May 2018 10:16:38 -0400 |
| parents | 8a33b442ecd9 |
| children | ad79e7bb1a9e |
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--- a/query_tabular.xml Mon Nov 06 23:20:29 2017 -0500 +++ b/query_tabular.xml Thu May 03 10:16:38 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="query_tabular" name="Query Tabular" version="2.0.0"> +<tool id="query_tabular" name="Query Tabular" version="3.0.0"> <description>using sqlite sql</description> <macros> @@ -17,7 +17,7 @@ cp '$add_to_database.withdb' '$workdb' && #end if #end if - python '$__tool_directory__/query_tabular.py' + python '$__tool_directory__/query_tabular.py' -d #if $save_db -s '$sqlitedb' #else @@ -88,6 +88,30 @@ #end if #set $jtbls += [$jtbl] #end for +#set $jstmts = [] +#for $i,$stmt in enumerate($modify_database.sql_stmts): + #set $jstmts += [str($stmt.sqlstmt)] +#end for +#if len($jstmts) > 0: + #set $jtbldef['sql_stmts'] = $jstmts +#end if +#set $jqueries = [] +#for $i,$query in enumerate($addqueries.queries): + #set $jquery = dict() + #set $jquery['query'] = str($query.sqlquery) + #set $jquery['result_file'] = 'results' + str($i) + '.tsv' + #if $query.query_result.header == 'yes': + #set $header_prefix = '' + #if $query.query_result.header_prefix: + #set $header_prefix = chr(int(str($query.query_result.header_prefix))) + #end if + #set $jquery['header'] = $header_prefix + #end if + #set $jqueries += [$jquery] +#end for +#if len($jqueries) > 0: + #set $jtbldef['queries'] = $jqueries +#end if #echo $json.dumps($jtbldef) </configfile> </configfiles> @@ -132,14 +156,24 @@ </repeat> </section> </repeat> + <section name="modify_database" expanded="false" title="Modify the database"> + <repeat name="sql_stmts" title="Database Manipulation SQL Statements" min="0"> + <param name="sqlstmt" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to modify the database"> + <help>These modify the SQLite database</help> + <sanitizer sanitize="False"/> + </param> + </repeat> + </section> <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history" help="SQLite to tabular tool can run additional queries on this database"/> - <param name="sqlquery" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to generate tabular output"> - <help>By default: tables are named: t1,t2,...,tn and columns in each table: c1,c2,...,cn</help> - <sanitizer sanitize="False"/> - <validator type="regex" message="">^(?ims)\s*select\s+.*\s+from\s+.*$</validator> - </param> + <expand macro="sql_query_input"/> <expand macro="result_results_header_line" /> + <section name="addqueries" expanded="false" title="Additional Queries"> + <repeat name="queries" title="Database Manipulation SQL Statements" min="0" max="3"> + <expand macro="sql_query_input"/> + <expand macro="result_results_header_line" /> + </repeat> + </section> </inputs> <outputs> <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}"> @@ -148,6 +182,15 @@ <data format="tabular" name="output" label="query results on ${on_string}"> <filter>not save_db or (sqlquery and len(sqlquery.strip()) > 0)</filter> </data> + <data format="tabular" name="output1" label="query 1 results on ${on_string}" from_work_dir="results0.tsv"> + <filter>len(addqueries['queries']) > 0</filter> + </data> + <data format="tabular" name="output2" label="query 2 results on ${on_string}" from_work_dir="results1.tsv"> + <filter>len(addqueries['queries']) > 1</filter> + </data> + <data format="tabular" name="output3" label="query 3 results on ${on_string}" from_work_dir="results2.tsv"> + <filter>len(addqueries['queries']) > 2</filter> + </data> </outputs> <tests> <test> @@ -448,6 +491,46 @@ <output name="output" file="psm_report_out2.tsv"/> </test> + <test> + <repeat name="tables"> + <param name="table" ftype="tabular" value="psm_report.tsv"/> + <section name="input_opts"> + <repeat name="linefilters"> + <conditional name="filter"> + <param name="filter_type" value="select_columns"/> + <param name="columns" value="1,3,2,6,14,19,23"/> + </conditional> + </repeat> + </section> + <section name="tbl_opts"> + <param name="table_name" value="PSMs"/> + <param name="column_names_from_first_line" value="True"/> + <param name="col_names" value="scan,,,,,,confidence"/> + </section> + </repeat> + <section name="modify_database"> + <repeat name="sql_stmts"> + <param name="sqlstmt" value="UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0"/> + </repeat> + </section> + <param name="sqlquery" value="SELECT scan,"m/z", "Precursor m/z Error [ppm]", Sequence, "Protein(s)", confidence FROM PSMs WHERE NOT re_search(', ',"Protein(s)")"/> + <conditional name="query_result"> + <param name="header" value="yes"/> + <param name="header_prefix" value="#"/> + </conditional> + <section name="addqueries"> + <repeat name="queries"> + <param name="sqlquery" value="SELECT * FROM psms WHERE confidence > 97.0"/> + <conditional name="query_result"> + <param name="header" value="yes"/> + <param name="header_prefix" value=""/> + </conditional> + </repeat> + </section> + <output name="output" file="psm_dbmod_output.tsv"/> + <output name="output1" file="psm_dbmod_output1.tsv"/> + </test> + </tests> <help><![CDATA[ =============