Mercurial > repos > jjohnson > query_tabular
comparison filter_tabular.xml @ 20:ab27c4bd14b9 draft
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author | jjohnson |
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date | Fri, 14 Jul 2017 11:39:27 -0400 |
parents | |
children | 357fe86f245d |
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19:9d9ab2c69014 | 20:ab27c4bd14b9 |
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1 <tool id="filter_tabular" name="Filter Tabular" version="5.0.0"> | |
2 <description></description> | |
3 | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 | |
8 <requirements> | |
9 </requirements> | |
10 <stdio> | |
11 <exit_code range="1:" /> | |
12 </stdio> | |
13 <command><![CDATA[ | |
14 python $__tool_directory__/filter_tabular.py | |
15 -i '$input' | |
16 -j '$filter_json' | |
17 -o '$output' | |
18 ]]></command> | |
19 <configfiles> | |
20 <configfile name="filter_json"> | |
21 #import json | |
22 @LINEFILTERS@ | |
23 #if $input_filters: | |
24 #echo $json.dumps($input_filters) | |
25 #end if | |
26 </configfile> | |
27 </configfiles> | |
28 <inputs> | |
29 <param name="input" type="data" format="tabular" label="Tabular Dataset to filter"/> | |
30 <expand macro="macro_line_filters" /> | |
31 </inputs> | |
32 <outputs> | |
33 <data format="tabular" name="output" /> | |
34 </outputs> | |
35 <tests> | |
36 <test> | |
37 <param name="input" ftype="tabular" value="pets.tsv"/> | |
38 <repeat name="linefilters"> | |
39 <param name="filter_type" value="comment"/> | |
40 <param name="comment_char" value="35"/> | |
41 </repeat> | |
42 <repeat name="linefilters"> | |
43 <param name="filter_type" value="append_line_num"/> | |
44 </repeat> | |
45 <repeat name="linefilters"> | |
46 <param name="filter_type" value="select_columns"/> | |
47 <param name="columns" value="7,2,3,4,1"/> | |
48 </repeat> | |
49 <repeat name="linefilters"> | |
50 <param name="filter_type" value="replace"/> | |
51 <param name="column" value="c4"/> | |
52 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/> | |
53 <param name="regex_replace" value="19\3-\2-\1"/> | |
54 </repeat> | |
55 <output name="output" file="filtered_people_results.tsv"/> | |
56 </test> | |
57 <test> | |
58 <param name="input" ftype="tabular" value="pets.tsv"/> | |
59 <repeat name="linefilters"> | |
60 <param name="filter_type" value="comment"/> | |
61 <param name="comment_char" value="35"/> | |
62 </repeat> | |
63 <repeat name="linefilters"> | |
64 <param name="filter_type" value="append_line_num"/> | |
65 </repeat> | |
66 <repeat name="linefilters"> | |
67 <param name="filter_type" value="select_columns"/> | |
68 <param name="columns" value="c7,c5,c6"/> | |
69 </repeat> | |
70 <repeat name="linefilters"> | |
71 <param name="filter_type" value="normalize"/> | |
72 <param name="columns" value="c2,c3"/> | |
73 <param name="separator" value=","/> | |
74 </repeat> | |
75 <output name="output" file="filtered_pets_results.tsv"/> | |
76 </test> | |
77 | |
78 </tests> | |
79 <help><![CDATA[ | |
80 ============== | |
81 Filter Tabular | |
82 ============== | |
83 | |
84 Filter a tabular dataset by applying line filters as it is being read. | |
85 Multiple filters may be used with each filter using the result of the previous filter. | |
86 | |
87 **Inputs** | |
88 | |
89 A tabular dataset. | |
90 | |
91 | |
92 **Outputs** | |
93 | |
94 A filtered tabular dataset. | |
95 | |
96 | |
97 @LINEFILTERS_HELP@ | |
98 | |
99 @LINEFILTERS_HELP_EXAMPLE@ | |
100 | |
101 ]]></help> | |
102 </tool> |