diff macros.xml @ 0:859064f07be4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
author iuc
date Tue, 18 Jul 2017 09:07:26 -0400
parents
children c1b700bc0150
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Jul 18 09:07:26 2017 -0400
@@ -0,0 +1,383 @@
+<macros>
+  <token name="@LINEFILTERS@">
+<![CDATA[
+  ## set linefilters to the 
+  #set $input_filters = []
+  #for $fi in $linefilters:
+    #if $fi.filter.filter_type == 'skip':
+      #set $skip_lines = None
+      #if str($fi.filter.skip_lines) != '':
+        #set $skip_lines = int($fi.filter.skip_lines)
+      #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0:
+        #set $skip_lines = int($tbl.table.metadata.comment_lines)
+      #end if
+      #if $skip_lines is not None:
+        #set $filter_dict = dict()
+        #set $filter_dict['filter'] = str($fi.filter.filter_type)
+        #set $filter_dict['count'] = $skip_lines
+        #silent $input_filters.append($filter_dict)
+      #end if
+    #elif $fi.filter.filter_type == 'comment':
+      #set $filter_dict = dict()
+      #set $filter_dict['filter'] = 'regex'
+      #set $filter_dict['pattern'] = '^(%s).*$' % '|'.join([chr(int(x)).replace('|','[|]') for x in (str($fi.filter.comment_char)).split(',')])
+      #set $filter_dict['action'] = 'exclude_match'
+      #silent $input_filters.append($filter_dict)
+    #elif $fi.filter.filter_type == 'regex':
+      #set $filter_dict = dict()
+      #set $filter_dict['filter'] = str($fi.filter.filter_type)
+      #set $filter_dict['pattern'] = str($fi.filter.regex_pattern)
+      #set $filter_dict['action'] = str($fi.filter.regex_action)
+      #silent $input_filters.append($filter_dict)
+    #elif $fi.filter.filter_type == 'select_columns':
+      #set $filter_dict = dict()
+      #set $filter_dict['filter'] = str($fi.filter.filter_type)
+      #set $filter_dict['columns'] = [int(str($ci).replace('c','')) for $ci in str($fi.filter.columns).split(',')]
+      #silent $input_filters.append($filter_dict)
+    #elif $fi.filter.filter_type == 'replace':
+      #set $filter_dict = dict()
+      #set $filter_dict['filter'] = str($fi.filter.filter_type)
+      #set $filter_dict['column'] = int(str($fi.filter.column).replace('c',''))
+      #set $filter_dict['pattern'] = str($fi.filter.regex_pattern)
+      #set $filter_dict['replace'] = str($fi.filter.regex_replace)
+      #silent $input_filters.append($filter_dict)
+    #elif str($fi.filter.filter_type).endswith('pend_line_num'):
+      #set $filter_dict = dict()
+      #set $filter_dict['filter'] = str($fi.filter.filter_type)
+      #silent $input_filters.append($filter_dict)
+    #elif str($fi.filter.filter_type).endswith('pend_text'):
+      #set $filter_dict = dict()
+      #set $filter_dict['filter'] = str($fi.filter.filter_type)
+      #set $filter_dict['column_text'] = str($fi.filter.column_text)
+      #silent $input_filters.append($filter_dict)
+    #elif $fi.filter.filter_type == 'normalize':
+      #set $filter_dict = dict()
+      #set $filter_dict['filter'] = str($fi.filter.filter_type)
+      #set $filter_dict['columns'] = [int(str($ci).replace('c','')) for $ci in str($fi.filter.columns).split(',')]
+      #set $filter_dict['separator'] = str($fi.filter.separator)
+      #silent $input_filters.append($filter_dict)
+    #end if
+  #end for
+]]>
+  </token>
+  <xml name="macro_line_filters">
+                <repeat name="linefilters" title="Filter Tabular Input Lines">
+                    <conditional name="filter">
+                        <param name="filter_type" type="select" label="Filter By">
+                            <option value="skip">skip leading lines</option>
+                            <option value="comment">comment char</option>
+                            <option value="regex">by regex expression matching</option>
+                            <option value="select_columns">select columns</option>
+                            <option value="replace">regex replace value in column</option>
+                            <option value="prepend_line_num">prepend a line number column</option>
+                            <option value="append_line_num">append a line number column</option>
+                            <option value="prepend_text">prepend a column with the given text</option>
+                            <option value="append_text">append a column with the given text</option>
+                            <option value="normalize">normalize list columns, replicates row for each item in list</option>
+                        </param>
+                        <when value="skip">
+                             <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines" 
+                                 help="Leave blank to use the comment lines metadata for this dataset" />
+                        </when>
+                        <when value="comment">
+                            <param name="comment_char" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are skipped">
+                                <option value="62">&gt;</option>
+                                <option value="64">@</option>
+                                <option value="43">+</option>
+                                <option value="60">&lt;</option>
+                                <option value="42">*</option>
+                                <option value="45">-</option>
+                                <option value="61">=</option>
+                                <option value="124">|</option>
+                                <option value="63">?</option>
+                                <option value="36">$</option>
+                                <option value="46">.</option>
+                                <option value="58">:</option>
+                                <option value="38">&amp;</option>
+                                <option value="37">%</option>
+                                <option value="94">^</option>
+                                <option value="35">&#35;</option>
+                                <option value="33">!</option>
+                            </param>
+                        </when>
+                        <when value="prepend_line_num"/>
+                        <when value="append_line_num"/>
+                        <when value="prepend_text">
+                            <param name="column_text" type="text" value="" label="text for column">
+                            </param>
+                        </when>
+                        <when value="append_text">
+                            <param name="column_text" type="text" value="" label="text for column">
+                            </param>
+                        </when>
+                        <when value="regex">
+                            <param name="regex_pattern" type="text" value="" label="regex pattern">
+                                <sanitizer sanitize="False"/>
+                            </param>
+                            <param name="regex_action" type="select" label="action for regex match">
+                                <option value="exclude_match">exclude line on pattern match</option>
+                                <option value="include_match">include line on pattern match</option>
+                                <option value="exclude_find">exclude line if pattern found</option>
+                                <option value="include_find">include line if pattern found</option>
+                            </param>
+                        </when>
+                        <when value="select_columns">
+                            <param name="columns" type="text" value="" label="enter column numbers to keep"
+                                help="example: 1,4,2 or c1,c4,c2(selects the first,fourth, and second columns)">
+                                <validator type="regex" message="Column ordinal positions separated by commas">^(c?[1-9]\d*)(,c?[1-9]\d*)*$</validator>
+                            </param>
+                        </when>
+                        <when value="replace">
+                            <param name="column" type="text" value="" label="enter column number to replace"
+                                help="example: 1 or c1 (selects the first column)">
+                                <validator type="regex" message="Column ordinal position separated by commas">^(c?[1-9]\d*)$</validator>
+                            </param>
+                            <param name="regex_pattern" type="text" value="" label="regex pattern">
+                                <sanitizer sanitize="False"/>
+                            </param>
+                            <param name="regex_replace" type="text" value="" label="replacement expression">
+                                <sanitizer sanitize="False"/>
+                            </param>
+                        </when>
+                        <when value="normalize">
+                            <param name="columns" type="text" value="" label="enter column numbers to normalize">
+                                <help><![CDATA[
+                                example: 2,4 or c2,c4 (selects the second, and fourth columns)
+                                If multiple columns are selected, they should have the same length and separator on each line
+                                ]]></help>
+                                <validator type="regex" message="Column ordinal positions separated by commas">^(c?[1-9]\d*)(,c?[1-9]\d*)*$</validator>
+                            </param>
+                            <param name="separator" type="text" value="," label="List item delimiter in column">
+                                <sanitizer sanitize="False"/>
+                                <validator type="regex" message="Anything but TAB or Newline">^[^\t\n\r\f\v]+$</validator>
+                            </param>
+                        </when>
+                    </conditional>
+                </repeat>
+  </xml>
+
+  <token name="@LINEFILTERS_HELP@">
+<![CDATA[
+**Input Line Filters**
+
+  As a tabular file is being read, line filters may be applied.  
+
+  ::
+
+  - skip leading lines              skip the first *number* of lines
+  - comment char                    omit any lines that start with the specified comment character 
+  - by regex expression matching    *include/exclude* lines the match the regex expression 
+  - select columns                  choose to include only selected columns in the order specified 
+  - regex replace value in column   replace a field in a column using a regex substitution (good for date reformatting)
+  - prepend a line number column    each line has the ordinal value of the line read by this filter as the first column
+  - append a line number column     each line has the ordinal value of the line read by this filter as the last column
+  - prepend a text column           each line has the text string as the first column
+  - append a text column            each line has the text string as the last column
+  - normalize list columns          replicates the line for each item in the specified list *columns*
+]]>
+  </token>
+
+  <token name="@LINEFILTERS_HELP_EXAMPLE@">
+<![CDATA[
+**Line Filtering Example** 
+  *(Six filters are applied as the following file is read)*
+
+  ::
+
+    Input Tabular File:
+
+    #People with pets
+    Pets FirstName           LastName   DOB       PetNames  PetType
+    2    Paula               Brown      24/05/78  Rex,Fluff dog,cat
+    1    Steven              Jones      04/04/74  Allie     cat
+    0    Jane                Doe        24/05/78  
+    1    James               Smith      20/10/80  Spot
+
+
+    Filter 1 - append a line number column:
+
+    #People with pets                                                 1
+    Pets FirstName           LastName   DOB       PetNames  PetType   2
+    2    Paula               Brown      24/05/78  Rex,Fluff dog,cat   3
+    1    Steven              Jones      04/04/74  Allie     cat       4
+    0    Jane                Doe        24/05/78                      5
+    1    James               Smith      20/10/80  Spot                6
+
+    Filter 2 - by regex expression matching [include]: '^\d+' (include lines that start with a number) 
+
+    2    Paula               Brown      24/05/78  Rex,Fluff dog,cat   3
+    1    Steven              Jones      04/04/74  Allie     cat       4
+    0    Jane                Doe        24/05/78                      5
+    1    James               Smith      20/10/80  Spot                6
+
+    Filter 3 - append a line number column:
+
+    2    Paula               Brown      24/05/78  Rex,Fluff dog,cat   3  1
+    1    Steven              Jones      04/04/74  Allie     cat       4  2
+    0    Jane                Doe        24/05/78                      5  3
+    1    James               Smith      20/10/80  Spot                6  4
+
+    Filter 4 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format) 
+
+    2    Paula               Brown      1978-05-24  Rex,Fluff dog,cat   3  1
+    1    Steven              Jones      1974-04-04  Allie     cat       4  2
+    0    Jane                Doe        1978-05-24                      5  3
+    1    James               Smith      1980-10-20  Spot                6  4
+
+    Filter 5 - normalize list columns[5,6]:
+
+    2    Paula               Brown      1978-05-24  Rex       dog       3  1
+    2    Paula               Brown      1978-05-24  Fluff     cat       3  1
+    1    Steven              Jones      1974-04-04  Allie     cat       4  2
+    0    Jane                Doe        1978-05-24                      5  3
+    1    James               Smith      1980-10-20  Spot                6  4
+
+    Filter 6 - append a line number column:
+
+    2    Paula               Brown      1978-05-24  Rex       dog       3  1  1
+    2    Paula               Brown      1978-05-24  Fluff     cat       3  1  2
+    1    Steven              Jones      1974-04-04  Allie     cat       4  2  3
+    0    Jane                Doe        1978-05-24                      5  3  4
+    1    James               Smith      1980-10-20  Spot                6  4  5
+
+]]>
+  </token>
+
+  <token name="@QUERY_HELP@">
+<![CDATA[
+
+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
+.. _SQLite_functions: http://www.sqlite.org/docs.html
+
+
+]]>
+  </token>
+
+</macros>
+