Mercurial > repos > jjohnson > query_tabular

comparison query_tabular.xml @ 3:3e3b3c883bec draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty
author jjohnson
date Tue, 16 Feb 2016 09:34:30 -0500
parents f5df461a6b90
children 9d73dca48178
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2:f5df461a6b90 3:3e3b3c883bec
1 <tool id="query_tabular" name="Query Tabular" version="0.1.0"> 1 <tool id="query_tabular" name="Query Tabular" version="0.1.1">
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>
12 -s $sqlitedb 12 -s $sqlitedb
13 #else 13 #else
14 -s $workdb 14 -s $workdb
15 #end if 15 #end if
16 -j $table_json 16 -j $table_json
17 #*
18 ## #for $i,$tbl in enumerate($tables):
19 ## #if $tbl.table_name
20 ## #set $tname = $tbl.table_name
21 ## #else
22 ## #set $tname = 't' + str($i + 1)
23 ## #end if
24 ## #if $tbl.col_names:
25 ## #set $col_names = ':' + str($tbl.col_names)
26 ## #else
27 ## #set $col_names = ''
28 ## #end if
29 ## -t ${tbl.table}=${tname}${$col_names}
30 ## #end for
31 *#
32 #if $sqlquery: 17 #if $sqlquery:
33 -Q "$query_file" 18 -Q "$query_file"
34 $no_header 19 $no_header
35 -o $output 20 -o $output
36 #end if 21 #end if
53 #set $tname = 't' + str($i + 1) 38 #set $tname = 't' + str($i + 1)
54 #end if 39 #end if
55 #set $jtbl['table_name'] = $tname 40 #set $jtbl['table_name'] = $tname
56 #if $tbl.col_names: 41 #if $tbl.col_names:
57 #set $col_names = str($tbl.col_names) 42 #set $col_names = str($tbl.col_names)
43 #if $tbl.load_named_columns:
44 #set $jtbl['load_named_columns'] = True
45 #end if
58 #else 46 #else
59 #set $col_names = '' 47 #set $col_names = ''
60 #end if 48 #end if
61 #set $jtbl['column_names'] = $col_names 49 #set $jtbl['column_names'] = $col_names
62 #if str($tbl.skip_lines) != '': 50 #if str($tbl.skip_lines) != '':
75 <param name="table" type="data" format="tabular" label="Dataset"/> 63 <param name="table" type="data" format="tabular" label="Dataset"/>
76 <param name="table_name" type="text" value="" optional="true" label="Table name"> 64 <param name="table_name" type="text" value="" optional="true" label="Table name">
77 <help>By default, tables will be named: t1,t2,...,tn</help> 65 <help>By default, tables will be named: t1,t2,...,tn</help>
78 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator> 66 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator>
79 </param> 67 </param>
80 <!--
81 <param name="sel_cols" label="Include columns" type="data_column" multiple="true" data_ref="table" />
82 -->
83 <param name="col_names" type="text" value="" optional="true" label="Column names"> 68 <param name="col_names" type="text" value="" optional="true" label="Column names">
84 <help>By default, table columns will be named: c1,c2,c3,...,cn</help> 69 <help>By default, table columns will be named: c1,c2,c3,...,cn</help>
85 <validator type="regex" message="A List of separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores">^([A-Za-z]\w*)?(,([A-Za-z]\w*)?)*$</validator> 70 <sanitizer sanitize="False"/>
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>
86 </param> 72 </param>
73 <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load named columns into database"/>
87 <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines" help="Leave blank to use the datatype comment lines metadata" /> 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" />
88 </repeat> 75 </repeat>
89 <param name="sqlquery" type="text" area="true" size="10x80" value="" optional="true" label="SQL Query"> 76 <param name="sqlquery" type="text" area="true" size="10x80" value="" optional="true" label="SQL Query">
90 <help>By default, tables will be named: t1,t2,...,tn</help> 77 <help>By default, tables will be named: t1,t2,...,tn</help>
91 <sanitizer sanitize="False"/> 78 <sanitizer sanitize="False"/>