annotate macros.xml @ 14:3a6b78c39dca draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit eb95b169fd23c0c5d75abd6e54042d2c9a882539

<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 $filter_dict['columns'] = [int($c) for $c in str($fi.filter.columns).replace('c','').split(',')]
      #silent $input_filters.append($filter_dict)
    #elif $fi.filter.filter_type == 'select_column_slices':
      #set $filter_dict = dict()
      #set $filter_dict['filter'] = str($fi.filter.filter_type)
      #set $filter_dict['columns'] = [$c for $c in str($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)
      #if $fi.filter.add:
          #set $filter_dict['add'] = str($fi.filter.add)
      #end if
      #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 str($fi.filter.filter_type).endswith('pend_dataset_name'):
      #set $filter_dict = dict()
      #set $filter_dict['filter'] = str($fi.filter.filter_type).replace('dataset_name', 'text')
      #set $filter_dict['column_text'] = $dataset_name
      #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>
  <token name="@RESULT_HEADER@">
<![CDATA[
    #if $query_result.header == 'yes':
        #if $query_result.header_prefix:
            #set $header_prefix = chr(int(str($query_result.header_prefix)))
            --comment_char='$header_prefix'
        #end if
    #else
        --no_header
    #end if
]]>
  </token>
  <xml name="requirements">
      <requirements>
          <requirement type="package" version="3.7">python</requirement>
      </requirements>
  </xml>
  <xml name="comment_char_options">
        <option value="62">&gt;</option>
        <option value="64">@</option>
        <option value="43">+</option>
        <option value="60">&lt;</option>
        <option value="42">*</option>
        <option value="45">-</option>
        <option value="61">=</option>
        <option value="124">|</option>
        <option value="63">?</option>
        <option value="36">$</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" selected="true">&#35;</option>
        <option value="33">!</option>
  </xml>
  <xml name="result_results_header_line">
      <conditional name="query_result">
          <param name="header" type="select" label="include query result column headers">
              <option value="yes">Yes</option>
              <option value="no">No</option>
          </param>
          <when value="yes">
              <param name="header_prefix" type="select" optional="true" label="Prefix character for column_header line">
                  <option value="">no comment character prefix</option>
                  <expand macro="comment_char_options" />
              </param>
          </when>
          <when value="no"/>
      </conditional>
  </xml>
  <xml name="sql_query_input">
        <param name="sqlquery" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to generate tabular output">
            <help>By default: tables are named: t1,t2,...,tn and columns in each table: c1,c2,...,cn</help>
            <sanitizer sanitize="False"/>
            <validator type="regex" message="">(?ims)^\s*select\s+.*\s+from\s+.*$</validator>
        </param>
  </xml>
  <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="select_column_slices">select columns by indices/slices</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_dataset_name">prepend a column with the dataset name</option>
                            <option value="append_dataset_name">append a column with the dataset name</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">
                                <expand macro="comment_char_options" />
                            </param>
                        </when>
                        <when value="prepend_line_num"/>
                        <when value="append_line_num"/>
                        <when value="prepend_dataset_name"/>
                        <when value="append_dataset_name"/>
                        <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="select_column_slices">
                            <param name="columns" type="text" value="" label="enter indices or slices of the columns to keep">
                                <help><![CDATA[ Python offset indexes or slices.  Examples:
                                 <ul>
                                 <li>Column offset indexes: 0,3,1 (selects the first,fourth, and second columns)</li>
                                 <li>Negative column numbers: -1,-2 (selects the last, and second last columns)</li>
                                 <li>python slices ( slice(start, stop[, step]) select a range of columns): <li>
                                   <ul>
                                     <li>0:3 or :3 (selects the first 3 columns)</li>
                                     <li>3:5 (selects the fourth and fifth columns)</li>
                                     <li>2: (selects all columns after the second)</li>
                                     <li>-2: (selects the last 2 columns)</li>
                                     <li>2::-1 (selects the first 3 columns n reverse order: third,second,first)</li>
                                   </ul>
                                 </ul>
                                ]]></help>
                                <validator type="regex" message="Column ordinal positions separated by commas">^(-?[1-9]\d*|((-?\d+)?:(-?\d*(:-?\d*)?)))(,(-?[1-9]\d*|((-?\d+)?:(-?\d*(:-?\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">^(c?[1-9]\d*)$</validator>
                            </param>
                            <param name="regex_pattern" type="text" value="" label="regex pattern">
                                <sanitizer sanitize="False"/>
                            </param>
                            <param name="regex_replace" type="text" value="" label="replacement expression">
                                <sanitizer sanitize="False"/>
                            </param>
                            <param name="add" type="select" optional="true" label="Instead of replacing, Add as new column:">
                                <option value="prepend">prepend to beginning of row</option>
                                <option value="append">append to the end of row</option>
                                <option value="before">insert before column field</option>
                                <option value="after">insert after column field</option>
                            </param>
                        </when>
                        <when value="normalize">
                            <param name="columns" type="text" value="" label="enter column numbers to normalize">
                                <help><![CDATA[
                                example: 2,4 or c2,c4 (selects the second, and fourth columns)
                                If multiple columns are selected, they should have the same length and separator on each line
                                ]]></help>
                                <validator type="regex" message="Column ordinal positions separated by commas">^(c?[1-9]\d*)(,c?[1-9]\d*)*$</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 that match the regex expression 
    - select columns                    - choose to include only selected columns in the order specified 
    - select columns by indices/slices  - *indices or slices* of the columns to keep (python_list_ indexing)
    - regex replace value in column     - replace a field in a column using a regex substitution (good for date reformatting)
    - regex replace value in column     - add a new column using a regex substitution of a column value
    - 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
    - prepend the dataset name          - each line has the *dataset name* as the first column
    - append the dataset name           - each line has the *dataset name* as the last column
    - normalize list columns            - replicates the line for each item in the specified list *columns*

.. _python_list: https://docs.python.org/3/library/stdtypes.html#common-sequence-operations
]]>
  </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 - select columns by indices/slices: '1:6'

    Paula               Brown      1978-05-24  Rex       dog
    Paula               Brown      1978-05-24  Fluff     cat
    Steven              Jones      1974-04-04  Allie     cat
    Jane                Doe        1978-05-24               
    James               Smith      1980-10-20  Spot         

]]>
  </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      [e-mail]  1968-02-04 626 222-2222
    2           Steven     Goldfish   [e-mail] 1974-04-04 323 455-4545
    3           Paula      Brown      [e-mail]   1978-05-24 416 323-3232
    4           James      Smith      [e-mail]    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      [e-mail]  1968-02-04 626 222-2222
    2           Steven     Goldfish   [e-mail] 1974-04-04 323 455-4545
    3           Paula      Brown      [e-mail]   1978-05-24 416 323-3232
    4           James      Smith      [e-mail]    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
    =========== ========== ==========

  Math_ functions *( python math library: https://docs.python.org/3.6/library/math.html )*:

  acos(x), acosh(x), asin(x), asinh(x), atan(x), atanh(x), atan2(x, y), ceil(x), cos(x), cosh(x), degrees(x), exp(x), expm1(x), fabs(x), floor(x), fmod(x, y), log(b,x), log(x), log10(x), log1p(x), log2(x), mod(x, y), pow(x, y), radians(x), sin(x), sinh(x), sqrt(x), tan(x), tanh(x), trunc(x)


  ::

    Query:

    SELECT SaleAmount, floor(SaleAmount) as "dollars"
    FROM sales

  Results:
    
    ============  ========
      SaleAmount   dollars
    ============  ========
          100.22       100
           99.95        99
          122.95       122
          100.00       100
          555.55       555
    ============  ========
  

.. _Regular_expression: https://docs.python.org/3.9/library/re.html
.. _Math: https://docs.python.org/3.9/library/math.html
.. _SQLite: http://www.sqlite.org/index.html
.. _SQLite_functions: http://www.sqlite.org/docs.html


]]>
  </token>
  <xml name="citations">
    <citations>
      <citation type="doi">10.12688/f1000research.16450.1</citation>
      <yield />
    </citations>
  </xml>


</macros>