diff query_tabular.xml @ 0:926c62f7fa09 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 08:23:45 -0500
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children c7a1a686e42b
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/query_tabular.xml	Thu Jan 21 08:23:45 2016 -0500
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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'] = $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 &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"/>
+                <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 &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_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>