diff sqlite_to_tabular.xml @ 3:f079ea3884b3 draft default tip

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty
author jjohnson
date Thu, 21 Jan 2016 09:34:45 -0500
parents bc50a7b7f246
children
line wrap: on
line diff
--- a/sqlite_to_tabular.xml	Sun Oct 04 10:51:12 2015 -0400
+++ b/sqlite_to_tabular.xml	Thu Jan 21 09:34:45 2016 -0500
@@ -4,19 +4,18 @@
     <stdio>
         <exit_code range="1:" level="fatal" description="Error" />
     </stdio>
+    <command interpreter="python"><![CDATA[
+    sqlite_to_tabular.py 
+    --sqlitedb="$sqlitedb" 
+    --query_file="$query_file"
+    $no_header 
+    --output="$query_results"
+    ]]></command>
     <configfiles>
         <configfile name="query_file">
 $sqlquery
         </configfile>
     </configfiles>
-
-    <command interpreter="python">
-    sqlite_to_tabular.py 
-    --sqlitedb="$sqlitedb" 
-    --query_file="$query_file"
-    $no_header 
-    --output="$query_results"
-    </command>
     <inputs>
         <param name="sqlitedb" type="data" format="sqlite" label="SQLite Database"/>
         <param name="sqlquery" type="text" area="True" size="120x20" label="SQL query">
@@ -40,7 +39,64 @@
             </output>
         </test>
     </tests>
-    <help>
-        Outputs the results of a query on a SQLite Database as a tabular file. 
-    </help>
+    <help><![CDATA[
+Outputs the results of a query on a SQLite_ Database as a tabular file. 
+
+In addition to the standard SQLite_functions_ regular_expression_ functions are included.
+
+For example, with SQLite table "customers":
+
+    =========== ========== ========== ===================== ========== ============
+    #CustomerID FirstName  LastName   Email                 BirthDate  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
+    =========== ========== ========== ===================== ========== ============
+
+  ::
+
+    matching:      re_match('pattern',column) 
+
+    SELECT FirstName, LastName
+    FROM customers
+    WHERE re_match('^.*\.(net|org)$',Email)
+
+  Results:
+
+    =========== ==========
+    #FirstName  LastName
+    =========== ==========
+    Steven      Goldfish
+    Paula       Brown
+    =========== ==========
+
+
+  ::
+
+    searching:     re_search('pattern',column)
+    substituting:  re_sub('pattern','replacement,column)
+
+    SELECT FirstName, LastName, re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB"
+    FROM customers
+    WHERE re_search('[hp]er',Email)
+
+  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
+.. _SQLite_functions: http://www.sqlite.org/docs.html
+
+    ]]></help>
 </tool>