Mercurial > repos > iuc > query_tabular
diff query_tabular.xml @ 1:8a33b442ecd9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
| author | iuc |
|---|---|
| date | Fri, 18 Aug 2017 16:48:09 -0400 |
| parents | 3708ff0198b7 |
| children | 973f03d82c86 |
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--- a/query_tabular.xml Tue Jul 18 09:07:07 2017 -0400 +++ b/query_tabular.xml Fri Aug 18 16:48:09 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="query_tabular" name="Query Tabular" version="1.0.0"> +<tool id="query_tabular" name="Query Tabular" version="2.0.0"> <description>using sqlite sql</description> <macros> @@ -26,7 +26,7 @@ -j '$table_json' #if $sqlquery: -Q '$query_file' - $no_header + @RESULT_HEADER@ -o '$output' #end if ]]></command> @@ -54,6 +54,9 @@ #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 $tbl.tbl_opts.load_named_columns: @@ -104,6 +107,9 @@ <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</help> <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</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. @@ -119,8 +125,9 @@ <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> + <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+[^,"]*[]])?)*$</validator> + <sanitizer sanitize="False"/> </param> </repeat> </section> @@ -132,7 +139,7 @@ <sanitizer sanitize="False"/> <validator type="regex" message="">^(?ims)\s*select\s+.*\s+from\s+.*$</validator> </param> - <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers from tabular output"/> + <expand macro="result_results_header_line" /> </inputs> <outputs> <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}"> @@ -391,6 +398,56 @@ <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,"m/z", "Precursor m/z Error [ppm]", Sequence, "Protein(s)" FROM PSMs WHERE NOT re_search(', ',"Protein(s)")"/> + <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[ ============= @@ -406,6 +463,45 @@ @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**