comparison query_tabular.xml @ 1:8a33b442ecd9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845

0:3708ff0198b7

<tool id="query_tabular" name="Query Tabular" version="1.0.0">
    <description>using sqlite sql</description>

    <macros>
         <import>macros.xml</import>
    </macros>

        -s '$workdb'
        #end if
        -j '$table_json'
        #if $sqlquery:
          -Q '$query_file' 
          $no_header
          -o '$output'
        #end if
    ]]></command>
    <configfiles>
        <configfile name="query_file">

  ## #if $tbl.tbl_opts.sel_cols:
  ##   #set $jtbl['sel_cols'] = $tbl.tbl_opts.sel_cols el_cols
  ## #end if
  #if $tbl.tbl_opts.pkey_autoincr:
    #set $jtbl['pkey_autoincr'] = str($tbl.tbl_opts.pkey_autoincr)
  #end if
  #if $tbl.tbl_opts.col_names:
  #set $col_names = str($tbl.tbl_opts.col_names)
    #if $tbl.tbl_opts.load_named_columns:
      #set $jtbl['load_named_columns'] = True

            <section name="tbl_opts" expanded="false" title="Table Options">
                <param name="table_name" type="text" value="" optional="true" label="Specify Name for Table">
                    <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</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="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)">
                    <help>By default, table columns will be named: c1,c2,c3,...,cn  (column names for a table must be unique)
                          You can override the default names by entering a comma -separated list of names, e.g. ',name1,,,name2' would rename the second and fifth columns.
                    </help>
                    <sanitizer sanitize="False"/>

                        <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator>
                </param>
                <repeat name="indexes" title="Table Index">
                    <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/>
                    <param name="index_columns" type="text" value="" label="Index on Columns">
                        <help>Create an index on the column names: e,g, c1  or c2,c4</help>
                        <validator type="regex" message="Column name, separated by commes if more than one">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator>
                    </param>
                </repeat>
            </section>
        </repeat>
        <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history"

        <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>
        <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers from tabular output"/>
    </inputs>
    <outputs>
        <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}">
            <filter>save_db</filter>
        </data>

            </repeat>
            <param name="sqlquery" value="SELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'"/>
            <output name="output" file="pet_normalized_query_results.tsv"/>
        </test>

    </tests>
    <help><![CDATA[
=============
Query Tabular
=============

  An existing SQLite_ data base can be used as input, and any selected tabular datasets will be added as new tables in that data base.


@LINEFILTERS_HELP@


**Outputs**

  The results of a SQL query are output to the history as a tabular file.

1:8a33b442ecd9

<tool id="query_tabular" name="Query Tabular" version="2.0.0">
    <description>using sqlite sql</description>

    <macros>
         <import>macros.xml</import>
    </macros>

        -s '$workdb'
        #end if
        -j '$table_json'
        #if $sqlquery:
          -Q '$query_file' 
          @RESULT_HEADER@
          -o '$output'
        #end if
    ]]></command>
    <configfiles>
        <configfile name="query_file">

  ## #if $tbl.tbl_opts.sel_cols:
  ##   #set $jtbl['sel_cols'] = $tbl.tbl_opts.sel_cols el_cols
  ## #end if
  #if $tbl.tbl_opts.pkey_autoincr:
    #set $jtbl['pkey_autoincr'] = str($tbl.tbl_opts.pkey_autoincr)
  #end if
  #if $tbl.tbl_opts.column_names_from_first_line:
    #set $jtbl['firstlinenames'] = True
  #end if
  #if $tbl.tbl_opts.col_names:
  #set $col_names = str($tbl.tbl_opts.col_names)
    #if $tbl.tbl_opts.load_named_columns:
      #set $jtbl['load_named_columns'] = True

            <section name="tbl_opts" expanded="false" title="Table Options">
                <param name="table_name" type="text" value="" optional="true" label="Specify Name for Table">
                    <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</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="column_names_from_first_line" type="boolean" truevalue="True" falsevalue="False" checked="false" 
                    label="Use first line as column names"
                    help="The names will be quoted if they are not valid SQLite column names."/>
                <param name="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)">
                    <help>By default, table columns will be named: c1,c2,c3,...,cn  (column names for a table must be unique)
                          You can override the default names by entering a comma -separated list of names, e.g. ',name1,,,name2' would rename the second and fifth columns.
                    </help>
                    <sanitizer sanitize="False"/>

                        <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator>
                </param>
                <repeat name="indexes" title="Table Index">
                    <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/>
                    <param name="index_columns" type="text" value="" label="Index on Columns">
                        <help>Create an index on the column names: e.g. for default column names:  c1  or c2,c4 ( use the names you gave for columns)</help>
                        <validator type="regex" message="Column name, separated by commes if more than one">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator>
                        <sanitizer sanitize="False"/>
                    </param>
                </repeat>
            </section>
        </repeat>
        <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history"

        <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>
        <expand macro="result_results_header_line" />
    </inputs>
    <outputs>
        <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}">
            <filter>save_db</filter>
        </data>

            </repeat>
            <param name="sqlquery" value="SELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'"/>
            <output name="output" file="pet_normalized_query_results.tsv"/>
        </test>

        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="psm_report.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">
                            <param name="filter_type" value="select_columns"/>
                            <param name="columns" value="1,3,2,6,14,19"/>
                        </conditional>
                    </repeat>
                </section>
                <section name="tbl_opts">
                    <param name="table_name" value="PSMs"/>
                    <param name="column_names_from_first_line" value="True"/>
                    <param name="col_names" value="Scan"/>
                </section>
            </repeat>
            <param name="sqlquery" value="SELECT * from PSMs"/>
            <conditional name="query_result">
                <param name="header" value="yes"/>
                <param name="header_prefix" value=""/>
            </conditional>
            <output name="output" file="psm_report_out1.tsv"/>
        </test>

        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="psm_report.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">
                            <param name="filter_type" value="select_columns"/>
                            <param name="columns" value="1,3,2,6,14,19"/>
                        </conditional>
                    </repeat>
                </section>
                <section name="tbl_opts">
                    <param name="table_name" value="PSMs"/>
                    <param name="column_names_from_first_line" value="True"/>
                    <param name="col_names" value="Scan"/>
                </section>
            </repeat>
            <param name="sqlquery" value="SELECT Scan,&quot;m/z&quot;, &quot;Precursor m/z Error [ppm]&quot;, Sequence, &quot;Protein(s)&quot; FROM PSMs WHERE NOT re_search(', ',&quot;Protein(s)&quot;)"/>
            <conditional name="query_result">
                <param name="header" value="yes"/>
                <param name="header_prefix" value=""/>
            </conditional>
            <output name="output" file="psm_report_out2.tsv"/>
        </test>

    </tests>
    <help><![CDATA[
=============
Query Tabular
=============

  An existing SQLite_ data base can be used as input, and any selected tabular datasets will be added as new tables in that data base.


@LINEFILTERS_HELP@

**Table Options**

  Specify Name for Table:

    - By default tables will be named: t1, t2, t3, etc.
 
    - **Specify Name for Table** 
      You can provide your own name for a database table, the name should begin with a letter and only contain letters, digits, or underscores. 
      The name should not be a SQLite key word: https://sqlite.org/lang_keywords.html


  There are several ways to name columns in a table:  

    - By default table columns will be named: c1, c2, c3, etc.

    - If **Use first line as column names** is selected, the first line is interpreted as column names, and not loaded into the table as a data row.  
      Any missing column name will be assigned cn where *n* is the ordinal position of the column, 
      e.g. a blank header for the second column would be named: c2.
      The column names will be quoted is they are not valid identifiers, 
      e.g. if they are SQLite keywords, or start with a non letter character, or contain a character other than a letter, digit, or underscore.
      The precedent for quoting is to enclose the identifier in double quotes, 
      else if it contains a double quote enclose in square brackets,
      else if it contains a square bracket enclose in grave accents.
      **NOTE:** that this is the first line after line filtering has been applied. 
      If a line filter *prepend a line number column* had been used, the name of the first column would be "1".
      You could rename that column using **Specify Column Names**

    - **Specify Column Names** (comma-separated list)
      This will override any previously assigned column names. 
      You can also choose to only load those columns for which you provided a name, 
      but that is better accomplished with the line filter: *select columns*. 


  **Table Index**

    Queries on larger tables can be much faster if indexes are specified.  
    In general, specifiy an index for table columns used in joins with other tables, 
    or on columns used in SQL query WHERE clauses or in GROUP BY clauses.


**Outputs**

  The results of a SQL query are output to the history as a tabular file.