Mercurial > repos > iuc > filter_tabular
comparison filter_tabular.xml @ 0:6fbd9d25ceef draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
author | iuc |
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date | Tue, 18 Jul 2017 09:06:47 -0400 |
parents | |
children | cd2a99849f8b |
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1 <tool id="filter_tabular" name="Filter Tabular" version="1.0.0"> | |
2 <description></description> | |
3 | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 | |
8 <requirements> | |
9 </requirements> | |
10 <command detect_errors="exit_code"><![CDATA[ | |
11 python '$__tool_directory__/filter_tabular.py' | |
12 -i '$input' | |
13 -j '$filter_json' | |
14 -o '$output' | |
15 ]]></command> | |
16 <configfiles> | |
17 <configfile name="filter_json"> | |
18 #import json | |
19 @LINEFILTERS@ | |
20 #if $input_filters: | |
21 #echo $json.dumps($input_filters) | |
22 #end if | |
23 </configfile> | |
24 </configfiles> | |
25 <inputs> | |
26 <param name="input" type="data" format="tabular" label="Tabular Dataset to filter"/> | |
27 <expand macro="macro_line_filters" /> | |
28 </inputs> | |
29 <outputs> | |
30 <data format="tabular" name="output" /> | |
31 </outputs> | |
32 <tests> | |
33 <test> | |
34 <param name="input" ftype="tabular" value="pets.tsv"/> | |
35 <repeat name="linefilters"> | |
36 <conditional name="filter"> | |
37 <param name="filter_type" value="regex"/> | |
38 <param name="regex_pattern" value="^\d+"/> | |
39 <param name="regex_action" value="include_find"/> | |
40 </conditional> | |
41 </repeat> | |
42 <repeat name="linefilters"> | |
43 <conditional name="filter"> | |
44 <param name="filter_type" value="append_line_num"/> | |
45 </conditional> | |
46 </repeat> | |
47 <repeat name="linefilters"> | |
48 <conditional name="filter"> | |
49 <param name="filter_type" value="select_columns"/> | |
50 <param name="columns" value="7,2,3,4,1"/> | |
51 </conditional> | |
52 </repeat> | |
53 <repeat name="linefilters"> | |
54 <conditional name="filter"> | |
55 <param name="filter_type" value="replace"/> | |
56 <param name="column" value="c4"/> | |
57 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/> | |
58 <param name="regex_replace" value="19\3-\2-\1"/> | |
59 </conditional> | |
60 </repeat> | |
61 <output name="output" file="filtered_people_results.tsv"/> | |
62 </test> | |
63 <test> | |
64 <param name="input" ftype="tabular" value="pets.tsv"/> | |
65 <repeat name="linefilters"> | |
66 <conditional name="filter"> | |
67 <param name="filter_type" value="comment"/> | |
68 <param name="comment_char" value="35"/> | |
69 </conditional> | |
70 </repeat> | |
71 <repeat name="linefilters"> | |
72 <conditional name="filter"> | |
73 <param name="filter_type" value="regex"/> | |
74 <param name="regex_pattern" value="^\d+"/> | |
75 <param name="regex_action" value="include_find"/> | |
76 </conditional> | |
77 </repeat> | |
78 <repeat name="linefilters"> | |
79 <conditional name="filter"> | |
80 <param name="filter_type" value="append_line_num"/> | |
81 </conditional> | |
82 </repeat> | |
83 <repeat name="linefilters"> | |
84 <conditional name="filter"> | |
85 <param name="filter_type" value="select_columns"/> | |
86 <param name="columns" value="c7,c5,c6"/> | |
87 </conditional> | |
88 </repeat> | |
89 <repeat name="linefilters"> | |
90 <conditional name="filter"> | |
91 <param name="filter_type" value="normalize"/> | |
92 <param name="columns" value="c2,c3"/> | |
93 <param name="separator" value=","/> | |
94 </conditional> | |
95 </repeat> | |
96 <repeat name="linefilters"> | |
97 <conditional name="filter"> | |
98 <param name="filter_type" value="regex"/> | |
99 <param name="regex_pattern" value="^\d+\t\t"/> | |
100 <param name="regex_action" value="exclude_match"/> | |
101 </conditional> | |
102 </repeat> | |
103 <output name="output" file="filtered_pets_results.tsv"/> | |
104 </test> | |
105 | |
106 </tests> | |
107 <help><![CDATA[ | |
108 ============== | |
109 Filter Tabular | |
110 ============== | |
111 | |
112 Filter a tabular dataset by applying line filters as it is being read. | |
113 Multiple filters may be used with each filter using the result of the previous filter. | |
114 | |
115 **Inputs** | |
116 | |
117 A tabular dataset. | |
118 | |
119 | |
120 **Outputs** | |
121 | |
122 A filtered tabular dataset. | |
123 | |
124 | |
125 @LINEFILTERS_HELP@ | |
126 | |
127 @LINEFILTERS_HELP_EXAMPLE@ | |
128 | |
129 ]]></help> | |
130 </tool> |