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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit eefe7cbd5c59de67db7574847bb91e4a404adc03-dirty
| author | jjohnson |
|---|---|
| date | Fri, 12 Feb 2016 07:27:49 -0500 |
| parents | 926c62f7fa09 |
| children | f5df461a6b90 |
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<tool id="query_tabular" name="Query Tabular" version="0.1.0"> <description>using sqlite sql</description> <requirements> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command interpreter="python"><![CDATA[ query_tabular.py #if $save_db -s $sqlitedb #else -s $workdb #end if -j $table_json #* ## #for $i,$tbl in enumerate($tables): ## #if $tbl.table_name ## #set $tname = $tbl.table_name ## #else ## #set $tname = 't' + str($i + 1) ## #end if ## #if $tbl.col_names: ## #set $col_names = ':' + str($tbl.col_names) ## #else ## #set $col_names = '' ## #end if ## -t ${tbl.table}=${tname}${$col_names} ## #end for *# #if $sqlquery: -Q "$query_file" $no_header -o $output #end if ]]></command> <configfiles> <configfile name="query_file"> $sqlquery </configfile> <configfile name="table_json"> #import json #set $jtbldef = dict() #set $jtbls = [] #set $jtbldef['tables'] = $jtbls #for $i,$tbl in enumerate($tables): #set $jtbl = dict() #set $jtbl['file_path'] = str($tbl.table) #if $tbl.table_name #set $tname = str($tbl.table_name) #else #set $tname = 't' + str($i + 1) #end if #set $jtbl['table_name'] = $tname #if $tbl.col_names: #set $col_names = str($tbl.col_names) #else #set $col_names = '' #end if #set $jtbl['column_names'] = $col_names #if str($tbl.skip_lines) != '': #set $jtbl['comment_lines'] = int($tbl.skip_lines) #elif $tbl.table.metadata.comment_lines > 0: #set $jtbl['comment_lines'] = int($tbl.table.metadata.comment_lines) #end if #set $jtbls += [$jtbl] #end for #echo $json.dumps($jtbldef) </configfile> </configfiles> <inputs> <param name="workdb" type="hidden" value="workdb.sqlite" label=""/> <repeat name="tables" title="Add tables" min="1"> <param name="table" type="data" format="tabular" label="Dataset"/> <param name="table_name" type="text" value="" optional="true" label="Table name"> <help>By default, tables will be named: t1,t2,...,tn</help> <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator> </param> <!-- <param name="sel_cols" label="Include columns" type="data_column" multiple="true" data_ref="table" /> --> <param name="col_names" type="text" value="" optional="true" label="Column names"> <help>By default, table columns will be named: c1,c2,c3,...,cn</help> <validator type="regex" message="A List of separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores">^([A-Za-z]\w*)?(,([A-Za-z]\w*)?)*$</validator> </param> <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines" help="Leave blank to use the datatype comment lines metadata" /> </repeat> <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> </param> <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers"/> <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database"/> </inputs> <outputs> <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}"> <filter>save_db or not (sqlquery and len(sqlquery) > 0)</filter> </data> <data format="tabular" name="output" label="query results on ${on_string}"> <filter>sqlquery and len(sqlquery) > 0</filter> </data> </outputs> <tests> <test> <repeat name="tables"> <param name="table" ftype="tabular" value="customers.tsv"/> <param name="table_name" value="customers"/> <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/> </repeat> <repeat name="tables"> <param name="table" ftype="tabular" value="sales.tsv"/> <param name="table_name" value="sales"/> <param name="col_names" value="CustomerID,Date,SaleAmount"/> </repeat> <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> <test> <repeat name="tables"> <param name="table" ftype="tabular" value="customers.tsv"/> <param name="col_names" value=",FirstName,LastName,,DOB,"/> </repeat> <repeat name="tables"> <param name="table" ftype="tabular" value="sales.tsv"/> </repeat> <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> <test> <repeat name="tables"> <param name="table" ftype="tabular" value="customers.tsv"/> <param name="col_names" value=",FirstName,LastName,,BirthDate,"/> </repeat> <param name="sqlquery" value="select FirstName,LastName,re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB" from t1 WHERE re_search('[hp]er',c4)"/> <output name="output" file="regex_results.tsv"/> </test> <test> <repeat name="tables"> <param name="table" ftype="tabular" value="IEDB.tsv"/> <param name="table_name" value="iedb"/> <param name="col_names" value="ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank"/> </repeat> <repeat name="tables"> <param name="table" ftype="tabular" value="netMHC_summary.tsv"/> <param name="table_name" value="mhc_summary"/> <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/> </repeat> <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> </tests> <help><![CDATA[ ============= Query Tabular ============= **Inputs** Loads tabular datasets into a SQLite_ data base. **Outputs** The results of a SQL query are output to the history as a tabular file. The SQLite_ data base can also be saved and output as a dataset in the history. For help in using SQLite_ see: http://www.sqlite.org/docs.html **NOTE:** input for SQLite dates input field must be in the format: *YYYY-MM-DD* for example: 2015-09-30 See: http://www.sqlite.org/lang_datefunc.html **Example** Given 2 tabular datasets: *customers* and *sales* Dataset *customers* Table name: "customers" Column names: "CustomerID,FirstName,LastName,Email,DOB,Phone" =========== ========== ========== ===================== ========== ============ #CustomerID FirstName LastName Email DOB Phone =========== ========== ========== ===================== ========== ============ 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888 =========== ========== ========== ===================== ========== ============ Dataset *sales* Table name: "sales" Column names: "CustomerID,Date,SaleAmount" ============= ============ ============ #CustomerID Date SaleAmount ============= ============ ============ 2 2004-05-06 100.22 1 2004-05-07 99.95 3 2004-05-07 122.95 3 2004-05-13 100.00 4 2004-05-22 555.55 ============= ============ ============ The query :: SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC; Produces this tabular output: ========== ======== ========== #FirstName LastName TotalSales ========== ======== ========== James Smith 555.55 Paula Brown 222.95 Steven Goldfish 100.22 John Smith 99.95 ========== ======== ========== If the optional Table name and Column names inputs are not used, the query would be: :: SELECT t1.c2 as "FirstName", t1.c3 as "LastName", sum(t2.c3) as "TotalSales" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC; You can selectively name columns, e.g. on the customers input you could just name columns 2,3, and 5: Column names: ,FirstName,LastName,,BirthDate Results in the following data base table =========== ========== ========== ===================== ========== ============ #c1 FirstName LastName c4 BirthDate c6 =========== ========== ========== ===================== ========== ============ 1 John Smith John.Smith@yahoo.com 1968-02-04 626 222-2222 2 Steven Goldfish goldfish@fishhere.net 1974-04-04 323 455-4545 3 Paula Brown pb@herowndomain.org 1978-05-24 416 323-3232 4 James Smith jim@supergig.co.uk 1980-10-20 416 323-8888 =========== ========== ========== ===================== ========== ============ Regular_expression_ functions are included for: :: matching: re_match('pattern',column) SELECT t1.FirstName, t1.LastName FROM t1 WHERE re_match('^.*\.(net|org)$',c4) Results: =========== ========== #FirstName LastName =========== ========== Steven Goldfish Paula Brown =========== ========== :: searching: re_search('pattern',column) substituting: re_sub('pattern','replacement,column) SELECT t1.FirstName, t1.LastName, re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB" FROM t1 WHERE re_search('[hp]er',c4) Results: =========== ========== ========== #FirstName LastName DOB =========== ========== ========== Steven Goldfish 04/04/74 Paula Brown 24/05/78 James Smith 20/10/80 =========== ========== ========== .. _Regular_expression: https://docs.python.org/release/2.7/library/re.html .. _SQLite: http://www.sqlite.org/index.html ]]></help> </tool>