query_tabular: query_tabular.xml comparison

comparison query_tabular.xml @ 4:afdbc7198353 draft

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty

author	jjohnson
date	Thu, 21 Jan 2016 08:09:36 -0500
parents	ffa5e34a55c1
children	727620f718c2

comparison

equal deleted inserted replaced

-:ffa5e34a55c1
+:afdbc7198353
 <requirements>
 </requirements>
 <stdio>
 <exit_code range="1:" />
 </stdio>
-<configfiles>
-<configfile name="query_file">
-$sqlquery
-</configfile>
-</configfiles>
 <command interpreter="python"><![CDATA[
 query_tabular.py
 #if $save_db
 -s $sqlitedb
 #else
 -s $workdb
 #end if
-#for $i,$tbl in enumerate($tables):
+-j $table_json
-#if $tbl.table_name
+#*
-#set $tname = $tbl.table_name
+##          #for $i,$tbl in enumerate($tables):
-#else
+##            #if $tbl.table_name
-#set $tname = 't' + str($i + 1)
+##            #set $tname = $tbl.table_name
-#end if
+##            #else
-#if $tbl.col_names:
+##            #set $tname = 't' + str($i + 1)
-#set $col_names = ':' + str($tbl.col_names)
+##            #end if
-#else
+##            #if $tbl.col_names:
-#set $col_names = ''
+##            #set $col_names = ':' + str($tbl.col_names)
-#end if
+##            #else
--t ${tbl.table}=${tname}${$col_names}
+##            #set $col_names = ''
-#end for
+##            #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'] = $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">
 -->
 <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 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">
+<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">
+<data format="tabular" name="output" label="query results on ${on_string}">
 <filter>sqlquery and len(sqlquery) > 0</filter>
 </data>
 </outputs>
 <tests>
 <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 &quot;TotalSales&quot; 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"/>
 </repeat>
 <repeat name="tables">
 <param name="table" ftype="tabular" value="sales.tsv"/>
 </repeat>
 <param name="sqlquery" value="SELECT FirstName,LastName,sum(t2.c3) as &quot;TotalSales&quot; 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 &quot;DOB&quot; 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" 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[
 =============
 Column names: ,FirstName,LastName,,BirthDate
 Results in the following data base table
 =========== ========== ========== ===================== ========== ============
-#c1         FirstName  LastName   c4                    BithDate   c6
+#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>

Mercurial > repos > jjohnson > query_tabular

comparison query_tabular.xml @ 4:afdbc7198353 draft