Mercurial > repos > jjohnson > query_tabular
comparison query_tabular.xml @ 4:9d73dca48178 draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty
| author | jjohnson |
|---|---|
| date | Tue, 19 Apr 2016 16:46:18 -0400 |
| parents | 3e3b3c883bec |
| children | 19ae309ec53c |
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| 3:3e3b3c883bec | 4:9d73dca48178 |
|---|---|
| 1 <tool id="query_tabular" name="Query Tabular" version="0.1.1"> | 1 <tool id="query_tabular" name="Query Tabular" version="0.1.2"> |
| 2 <description>using sqlite sql</description> | 2 <description>using sqlite sql</description> |
| 3 | 3 |
| 4 <requirements> | 4 <requirements> |
| 5 </requirements> | 5 </requirements> |
| 6 <stdio> | 6 <stdio> |
| 30 #set $jtbls = [] | 30 #set $jtbls = [] |
| 31 #set $jtbldef['tables'] = $jtbls | 31 #set $jtbldef['tables'] = $jtbls |
| 32 #for $i,$tbl in enumerate($tables): | 32 #for $i,$tbl in enumerate($tables): |
| 33 #set $jtbl = dict() | 33 #set $jtbl = dict() |
| 34 #set $jtbl['file_path'] = str($tbl.table) | 34 #set $jtbl['file_path'] = str($tbl.table) |
| 35 #if $tbl.table_name | 35 #if $tbl.tbl_opts.table_name: |
| 36 #set $tname = str($tbl.table_name) | 36 #set $tname = str($tbl.tbl_opts.table_name) |
| 37 #else | 37 #else |
| 38 #set $tname = 't' + str($i + 1) | 38 #set $tname = 't' + str($i + 1) |
| 39 #end if | 39 #end if |
| 40 #set $jtbl['table_name'] = $tname | 40 #set $jtbl['table_name'] = $tname |
| 41 #if $tbl.col_names: | 41 ## #if $tbl.tbl_opts.sel_cols: |
| 42 #set $col_names = str($tbl.col_names) | 42 ## #set $jtbl['sel_cols'] = $tbl.tbl_opts.sel_cols el_cols |
| 43 #if $tbl.load_named_columns: | 43 ## #end if |
| 44 #if $tbl.tbl_opts.col_names: | |
| 45 #set $col_names = str($tbl.tbl_opts.col_names) | |
| 46 #if $tbl.tbl_opts.load_named_columns: | |
| 44 #set $jtbl['load_named_columns'] = True | 47 #set $jtbl['load_named_columns'] = True |
| 45 #end if | 48 #end if |
| 46 #else | 49 #else |
| 47 #set $col_names = '' | 50 #set $col_names = '' |
| 48 #end if | 51 #end if |
| 49 #set $jtbl['column_names'] = $col_names | 52 #set $jtbl['column_names'] = $col_names |
| 50 #if str($tbl.skip_lines) != '': | 53 #if str($tbl.tbl_opts.skip_lines) != '': |
| 51 #set $jtbl['comment_lines'] = int($tbl.skip_lines) | 54 #set $jtbl['comment_lines'] = int($tbl.tbl_opts.skip_lines) |
| 52 #elif $tbl.table.metadata.comment_lines > 0: | 55 #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0: |
| 53 #set $jtbl['comment_lines'] = int($tbl.table.metadata.comment_lines) | 56 #set $jtbl['comment_lines'] = int($tbl.table.metadata.comment_lines) |
| 57 #end if | |
| 58 #set $idx_unique = [] | |
| 59 #set $idx_non = [] | |
| 60 #for $idx in $tbl.tbl_opts.indexes: | |
| 61 #if $idx.unique: | |
| 62 #silent $idx_unique.append(str($idx.index_columns)) | |
| 63 #else: | |
| 64 #silent $idx_non.append(str($idx.index_columns)) | |
| 65 #end if | |
| 66 #end for | |
| 67 #if len($idx_unique) > 0: | |
| 68 #set $jtbl['unique'] = $idx_unique | |
| 69 #end if | |
| 70 #if len($idx_non) > 0: | |
| 71 #set $jtbl['index'] = $idx_non | |
| 54 #end if | 72 #end if |
| 55 #set $jtbls += [$jtbl] | 73 #set $jtbls += [$jtbl] |
| 56 #end for | 74 #end for |
| 57 #echo $json.dumps($jtbldef) | 75 #echo $json.dumps($jtbldef) |
| 58 </configfile> | 76 </configfile> |
| 59 </configfiles> | 77 </configfiles> |
| 60 <inputs> | 78 <inputs> |
| 61 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/> | 79 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/> |
| 62 <repeat name="tables" title="Add tables" min="1"> | 80 <repeat name="tables" title="Add tables" min="1"> |
| 63 <param name="table" type="data" format="tabular" label="Dataset"/> | 81 <param name="table" type="data" format="tabular" label="Dataset"/> |
| 64 <param name="table_name" type="text" value="" optional="true" label="Table name"> | 82 <section name="tbl_opts" expanded="false" title="Table Options"> |
| 65 <help>By default, tables will be named: t1,t2,...,tn</help> | 83 <param name="table_name" type="text" value="" optional="true" label="Table name"> |
| 66 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator> | 84 <help>By default, tables will be named: t1,t2,...,tn</help> |
| 67 </param> | 85 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator> |
| 68 <param name="col_names" type="text" value="" optional="true" label="Column names"> | 86 </param> |
| 69 <help>By default, table columns will be named: c1,c2,c3,...,cn</help> | 87 <param name="col_names" type="text" value="" optional="true" label="Column names"> |
| 70 <sanitizer sanitize="False"/> | 88 <help>By default, table columns will be named: c1,c2,c3,...,cn</help> |
| 71 <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+[^,"]*[]])?)*$</validator> | 89 <sanitizer sanitize="False"/> |
| 72 </param> | 90 <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator> |
| 73 <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load named columns into database"/> | 91 </param> |
| 74 <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines" help="Leave blank to use the datatype comment lines metadata" /> | 92 <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load named columns into database"/> |
| 93 <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines" help="Leave blank to use the datatype comment lines metadata" /> | |
| 94 <repeat name="indexes"> | |
| 95 <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/> | |
| 96 <param name="index_columns" type="text" value="" label="Index on Columns"> | |
| 97 <help>Create an index on the column names: e,g, c1 or c2,c4</help> | |
| 98 <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+[^,"]*[]])?)*$</validator> | |
| 99 </param> | |
| 100 </repeat> | |
| 101 </section> | |
| 75 </repeat> | 102 </repeat> |
| 76 <param name="sqlquery" type="text" area="true" size="10x80" value="" optional="true" label="SQL Query"> | 103 <param name="sqlquery" type="text" area="true" size="10x80" value="" optional="true" label="SQL Query"> |
| 77 <help>By default, tables will be named: t1,t2,...,tn</help> | 104 <help>By default, tables will be named: t1,t2,...,tn</help> |
| 78 <sanitizer sanitize="False"/> | 105 <sanitizer sanitize="False"/> |
| 79 <validator type="regex" message="">^(?im)\s*select\s+.*\s+from\s+.*$</validator> | 106 <validator type="regex" message="">^(?ims)\s*select\s+.*\s+from\s+.*$</validator> |
| 80 </param> | 107 </param> |
| 81 <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers"/> | 108 <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers"/> |
| 82 | 109 |
| 83 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database"/> | 110 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database"/> |
| 84 </inputs> | 111 </inputs> |