Mercurial > repos > jjohnson > query_tabular

comparison query_tabular.xml @ 8:ae27dab228b8 draft

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author jjohnson
date Tue, 21 Feb 2017 12:59:26 -0500
parents 03842a4f71c6
children fd16243931d6
comparison
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7:72c32037fa1e 8:ae27dab228b8
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 </stdio> 8 </stdio>
9 <command><![CDATA[ 9 <command><![CDATA[
10 cat $query_file &&
10 #if $add_to_database.withdb: 11 #if $add_to_database.withdb:
11 #if $save_db: 12 #if $save_db:
12 cp "$add_to_database.withdb" "$save_db" && 13 cp "$add_to_database.withdb" "$sqlitedb" &&
13 #else: 14 #else:
14 cp "$add_to_database.withdb" "$workdb" && 15 cp "$add_to_database.withdb" "$workdb" &&
15 #end if 16 #end if
16 #end if 17 #end if
17 python $__tool_directory__/query_tabular.py 18 python $__tool_directory__/query_tabular.py
18 #if $save_db 19 #if $save_db
19 -s $sqlitedb 20 -s "$sqlitedb"
20 #else 21 #else
21 -s $workdb 22 -s $workdb
22 #end if 23 #end if
23 -j $table_json 24 -j $table_json
24 #if $sqlquery: 25 #if $sqlquery:
25 -Q "$query_file" 26 -Q "$query_file"
26 $no_header 27 $no_header
27 -o $output 28 -o $output
28 #end if 29 #end if
29 && cat $query_file
30 && cat $table_json
31 ]]></command> 30 ]]></command>
32 <configfiles> 31 <configfiles>
33 <configfile name="query_file"> 32 <configfile name="query_file">
34 $sqlquery 33 $sqlquery
35 </configfile> 34 </configfile>
78 #set $jtbl['index'] = $idx_non 77 #set $jtbl['index'] = $idx_non
79 #end if 78 #end if
80 #set $input_filters = [] 79 #set $input_filters = []
81 #for $fi in $tbl.input_opts.linefilters: 80 #for $fi in $tbl.input_opts.linefilters:
82 #if $fi.filter.filter_type == 'skip': 81 #if $fi.filter.filter_type == 'skip':
83 #if str($tbl.tbl_opts.skip_lines) != '': 82 #if str($fi.filter.skip_lines) != '':
84 #set $jtbl['comment_lines'] = int($fi.filter.skip_lines) 83 #set $jtbl['comment_lines'] = int($fi.filter.skip_lines)
85 #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0: 84 #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0:
86 #set $jtbl['comment_lines'] = int($tbl.table.metadata.comment_lines) 85 #set $jtbl['comment_lines'] = int($tbl.table.metadata.comment_lines)
87 #end if 86 #end if
88 #elif $fi.filter.filter_type == 'comment': 87 #elif $fi.filter.filter_type == 'comment':
120 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/> 119 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/>
121 <section name="add_to_database" expanded="false" title="Add tables to an existing database"> 120 <section name="add_to_database" expanded="false" title="Add tables to an existing database">
122 <param name="withdb" type="data" format="sqlite" optional="true" label="Add tables to this Database" 121 <param name="withdb" type="data" format="sqlite" optional="true" label="Add tables to this Database"
123 help="Make sure your added table names are not already in this database"/> 122 help="Make sure your added table names are not already in this database"/>
124 </section> 123 </section>
125 <repeat name="tables" title="Database Table" min="1"> 124 <repeat name="tables" title="Database Table" min="0">
126 <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/> 125 <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/>
127 <section name="input_opts" expanded="false" title="Filter Dataset Input"> 126 <section name="input_opts" expanded="false" title="Filter Dataset Input">
128 <repeat name="linefilters" title="Filter Tabular Input Lines"> 127 <repeat name="linefilters" title="Filter Tabular Input Lines">
129 <conditional name="filter"> 128 <conditional name="filter">
130 <param name="filter_type" type="select" label="Filter By"> 129 <param name="filter_type" type="select" label="Filter By">
135 <!-- 134 <!--
136 <option value="normalize">normalize list columns, replicates row for each item in list</option> 135 <option value="normalize">normalize list columns, replicates row for each item in list</option>
137 --> 136 -->
138 </param> 137 </param>
139 <when value="skip"> 138 <when value="skip">
140 <param name="skip_lines" type="integer" value="" min="0" label="Skip lines" 139 <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines"
141 help="Leave blank to use the comment lines metadata for this dataset" /> 140 help="Leave blank to use the comment lines metadata for this dataset" />
142 </when> 141 </when>
143 <when value="comment"> 142 <when value="comment">
144 <param name="comment_char" type="text" value="#" label="Comment line starting text"> 143 <param name="comment_char" type="text" value="#" label="Comment line starting text">
144 <sanitizer sanitize="False"/>
145 </param> 145 </param>
146 </when> 146 </when>
147 <when value="regex"> 147 <when value="regex">
148 <param name="regex_pattern" type="text" value="" label="regex pattern"> 148 <param name="regex_pattern" type="text" value="" label="regex pattern">
149 <sanitizer sanitize="False"/> 149 <sanitizer sanitize="False"/>