| Previous changeset 7:72c32037fa1e (2017-02-18) Next changeset 9:0ed75ed20c7e (2017-03-02) |
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modified:
query_tabular.py query_tabular.xml |
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| diff -r 72c32037fa1e -r ae27dab228b8 query_tabular.py --- a/query_tabular.py Sat Feb 18 08:35:35 2017 -0500 +++ b/query_tabular.py Tue Feb 21 12:59:26 2017 -0500 |
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| @@ -63,7 +63,7 @@ def __init__(self,source,filter_dict): self.source = source self.filter_dict = filter_dict - print >> sys.stderr, 'LineFilter %s' % filter_dict if filter_dict else 'NONE' + # print >> sys.stderr, 'LineFilter %s' % filter_dict if filter_dict else 'NONE' self.func = lambda l: l.rstrip('\r\n') if l else None if not filter_dict: return |
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| diff -r 72c32037fa1e -r ae27dab228b8 query_tabular.xml --- a/query_tabular.xml Sat Feb 18 08:35:35 2017 -0500 +++ b/query_tabular.xml Tue Feb 21 12:59:26 2017 -0500 |
| [ |
| @@ -7,16 +7,17 @@ <exit_code range="1:" /> </stdio> <command><![CDATA[ + cat $query_file && #if $add_to_database.withdb: #if $save_db: - cp "$add_to_database.withdb" "$save_db" && + cp "$add_to_database.withdb" "$sqlitedb" && #else: cp "$add_to_database.withdb" "$workdb" && #end if #end if python $__tool_directory__/query_tabular.py #if $save_db - -s $sqlitedb + -s "$sqlitedb" #else -s $workdb #end if @@ -26,8 +27,6 @@ $no_header -o $output #end if - && cat $query_file - && cat $table_json ]]></command> <configfiles> <configfile name="query_file"> @@ -80,7 +79,7 @@ #set $input_filters = [] #for $fi in $tbl.input_opts.linefilters: #if $fi.filter.filter_type == 'skip': - #if str($tbl.tbl_opts.skip_lines) != '': + #if str($fi.filter.skip_lines) != '': #set $jtbl['comment_lines'] = int($fi.filter.skip_lines) #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0: #set $jtbl['comment_lines'] = int($tbl.table.metadata.comment_lines) @@ -122,7 +121,7 @@ <param name="withdb" type="data" format="sqlite" optional="true" label="Add tables to this Database" help="Make sure your added table names are not already in this database"/> </section> - <repeat name="tables" title="Database Table" min="1"> + <repeat name="tables" title="Database Table" min="0"> <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/> <section name="input_opts" expanded="false" title="Filter Dataset Input"> <repeat name="linefilters" title="Filter Tabular Input Lines"> @@ -137,11 +136,12 @@ --> </param> <when value="skip"> - <param name="skip_lines" type="integer" value="" min="0" label="Skip lines" + <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" /> </when> <when value="comment"> <param name="comment_char" type="text" value="#" label="Comment line starting text"> + <sanitizer sanitize="False"/> </param> </when> <when value="regex"> |