Mercurial > repos > jjohnson > query_tabular
diff 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
| author | jjohnson |
|---|---|
| date | Wed, 20 Apr 2016 15:44:33 -0400 |
| parents | b7f149b4792f |
| children |
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--- a/query_tabular.xml Fri Apr 15 16:48:50 2016 -0400 +++ b/query_tabular.xml Wed Apr 20 15:44:33 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="query_tabular" name="Query Tabular" version="0.1.2"> +<tool id="query_tabular" name="Query Tabular" version="0.1.3"> <description>using sqlite sql</description> <requirements> @@ -41,6 +41,9 @@ ## #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 $tbl.tbl_opts.load_named_columns: @@ -77,21 +80,25 @@ </configfiles> <inputs> <param name="workdb" type="hidden" value="workdb.sqlite" label=""/> - <repeat name="tables" title="Add tables" min="1"> - <param name="table" type="data" format="tabular" label="Dataset"/> + <repeat name="tables" title="Database Table" min="1"> + <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/> <section name="tbl_opts" expanded="false" title="Table Options"> - <param name="table_name" type="text" value="" optional="true" label="Table name"> - <help>By default, tables will be named: t1,t2,...,tn</help> + <param name="table_name" type="text" value="" optional="true" label="Specify Name for Table"> + <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</help> <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator> </param> - <param name="col_names" type="text" value="" optional="true" label="Column names"> - <help>By default, table columns will be named: c1,c2,c3,...,cn</help> + <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+[^,"]*[]])?)*$</validator> </param> - <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load named columns into database"/> - <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines" help="Leave blank to use the datatype comment lines metadata" /> - <repeat name="indexes"> + <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load the columns you have named into database"/> + <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name" + help="Only creates this additional column when a name is entered. (This can not be the same name as any of the other columns in this table.)"> + <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</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> @@ -100,14 +107,13 @@ </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> + <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"/> - - <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database"/> + <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}"> @@ -186,6 +192,9 @@ 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