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comparison filter_tabular.xml @ 0:c0c0226e1c9c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
author iuc
date Tue, 18 Jul 2017 09:05:41 -0400
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-1:000000000000 0:c0c0226e1c9c
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>