Mercurial > repos > jjohnson > query_tabular
diff query_tabular.xml @ 2:ffa5e34a55c1
Uploaded
| author | jjohnson |
|---|---|
| date | Sun, 04 Oct 2015 10:52:21 -0400 |
| parents | 24f0911f75ee |
| children | afdbc7198353 |
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--- a/query_tabular.xml Sat Oct 03 09:23:08 2015 -0400 +++ b/query_tabular.xml Sun Oct 04 10:52:21 2015 -0400 @@ -6,7 +6,11 @@ <stdio> <exit_code range="1:" /> </stdio> - + <configfiles> + <configfile name="query_file"> +$sqlquery + </configfile> + </configfiles> <command interpreter="python"><![CDATA[ query_tabular.py #if $save_db @@ -27,8 +31,8 @@ #end if -t ${tbl.table}=${tname}${$col_names} #end for - #if $query: - -q "$query" + #if $sqlquery: + -Q "$query_file" $no_header -o $output #end if @@ -49,7 +53,7 @@ <validator type="regex" message="A List of separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores">^([A-Za-z]\w*)?(,([A-Za-z]\w*)?)*$</validator> </param> </repeat> - <param name="query" type="text" area="true" size="10x80" value="" optional="true" label="SQL Query"> + <param name="sqlquery" type="text" area="true" size="10x80" value="" optional="true" label="SQL Query"> <help>By default, tables will be named: t1,t2,...,tn</help> <sanitizer sanitize="False"/> <validator type="regex" message="">^(?i)\s*select\s+.*\s+from\s+.*$</validator> @@ -60,10 +64,10 @@ </inputs> <outputs> <data format="sqlite" name="sqlitedb" label="sqlite"> - <filter>save_db or not (query and len(query) > 0)</filter> + <filter>save_db or not (sqlquery and len(sqlquery) > 0)</filter> </data> <data format="tabular" name="output" label="query results"> - <filter>query and len(query) > 0</filter> + <filter>sqlquery and len(sqlquery) > 0</filter> </data> </outputs> <tests> @@ -79,7 +83,7 @@ <param name="table_name" value="sales"/> <param name="col_names" value="CustomerID,Date,SaleAmount"/> </repeat> - <param name="query" value="SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC"/> + <param name="sqlquery" value="SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC"/> <output name="output" file="sales_results.tsv"/> </test> @@ -91,7 +95,7 @@ <repeat name="tables"> <param name="table" ftype="tabular" value="sales.tsv"/> </repeat> - <param name="query" value="SELECT FirstName,LastName,sum(t2.c3) as "TotalSales" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;"/> + <param name="sqlquery" value="SELECT FirstName,LastName,sum(t2.c3) as "TotalSales" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;"/> <output name="output" file="sales_results.tsv"/> </test> @@ -106,7 +110,7 @@ <param name="table_name" value="mhc_summary"/> <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/> </repeat> - <param name="query" value="select iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level"/> + <param name="sqlquery" value="select iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level"/> <output name="output" file="query_results.tsv"/> </test>