comparison query_tabular.xml @ 10:98bd1e29d669 draft default tip

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty

9:b7f149b4792f

<tool id="query_tabular" name="Query Tabular" version="0.1.2">
    <description>using sqlite sql</description>

    <requirements>
    </requirements>
    <stdio>

  #end if
  #set $jtbl['table_name'] = $tname
  ## #if $tbl.tbl_opts.sel_cols:
  ##   #set $jtbl['sel_cols'] = $tbl.tbl_opts.sel_cols el_cols
  ## #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
    #end if

#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"/>
            <section name="tbl_opts" expanded="false" title="Table Options">
                <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*$</validator>
                </param>
                <param name="col_names" type="text" value="" optional="true" label="Column names">
                    <help>By default, table columns will be named: c1,c2,c3,...,cn</help>
                    <sanitizer sanitize="False"/>
                    <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator>
                </param>
                <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load named columns into database"/>
                <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 name="indexes">
                    <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+[^,"]*[]])?)*$</validator>
                    </param>
                </repeat>
            </section>
        </repeat>
        <param name="sqlquery" type="text" area="true" size="10x80" value="" optional="true" label="SQL Query">
                <help>By default, tables will be named: t1,t2,...,tn</help>
                <sanitizer sanitize="False"/>
                <validator type="regex" message="">^(?ims)\s*select\s+.*\s+from\s+.*$</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>

  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

10:98bd1e29d669

<tool id="query_tabular" name="Query Tabular" version="0.1.3">
    <description>using sqlite sql</description>

    <requirements>
    </requirements>
    <stdio>

  #end if
  #set $jtbl['table_name'] = $tname
  ## #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
    #end if

#echo $json.dumps($jtbldef)
        </configfile>
    </configfiles>
    <inputs>
        <param name="workdb" type="hidden" value="workdb.sqlite" label=""/>
        <repeat name="tables" title="Database Table" min="1">
            <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/>
            <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*$</validator>
                </param>
                <param name="col_names" type="text" value="" optional="true" label="Specify Column Names">
                    <help>By default, table columns will be named: c1,c2,c3,...,cn  (column names for a table must be unique)</help>
                    <sanitizer sanitize="False"/>
                    <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator>
                </param>
                <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load the columns you have named into database"/>
                <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name"
                       help="Only creates this additional column when a name is entered. (This can not be the same name as any of the other columns in this table.)">
                        <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator>
                </param>
                <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines" help="Leave blank to use the comment lines metadata for this dataset" />
                <repeat name="indexes" title="Table Index">
                    <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/>
                    <param name="index_columns" type="text" value="" label="Index on Columns">
                        <help>Create an index on the column names: e,g, c1  or c2,c4</help>
                        <validator type="regex" message="Column name, separated by commes if more than one">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</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="10x80" 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 or not (sqlquery and len(sqlquery) > 0)</filter>
        </data>

  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.  

    *(The* **SQLite to tabular** *tool can run additional queries on this database.)*



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