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comparison replace.xml @ 0:1d4ee4308d99 draft default tip

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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:16:05 -0400
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1 <tool id="csvtk_replace" name="csvtk-replace" version="@VERSION@+@GALAXY_VERSION@">
2 <description> data of selected columns by regular expression</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_cmd" />
8 <command detect_errors="exit_code"><![CDATA[
9
10 ###################
11 ## Start Command ##
12 ###################
13 csvtk replace --num-cpus "\${GALAXY_SLOTS:-1}"
14
15 ## Add additional flags as specified ##
16 #######################################
17 $ignore_case
18 $global_param.illegal_rows
19 $global_param.empty_rows
20 $global_param.header
21 $global_param.lazy_quotes
22
23 ## Set Tabular input/output flag if first input is tabular ##
24 #############################################################
25 #if $in_1.is_of_type("tabular"):
26 -t -T
27 #end if
28
29 ## Set input files ##
30 #####################
31 '$in_1'
32
33 ## Specify fields to use ##
34 ###########################
35 -F -f '${column_text.in_text}'
36
37 ## Specific Commands ##
38 #######################
39 -p '($pattern_string)'
40 -r '$replacement_string'
41
42 #if $input_kv
43 -k '$input_kv'
44 #end if
45
46 #if $fill.how_fill == "key"
47 -K
48 #elif $fill.how_fill == "string"
49 --key-miss-repl '$fill.fill_string'
50 #end if
51
52 ## To output ##
53 ###############
54 > replaced
55
56 ]]></command>
57 <inputs>
58 <expand macro="singular_input"/>
59 <expand macro="fields_input" />
60 <param name="pattern_string" type="text" argument="-p"
61 label="Pattern Regex"
62 help="Regex to search column for. Input is structured as '(YOUR_INPUT_HERE)' so if your regex was just a period it would look like '(.)' as an input.">
63 <expand macro="text_sanitizer" />
64 </param>
65 <param name="replacement_string" type="text" argument="-r"
66 label="Replacement String">
67 <help>
68 <![CDATA[
69 String to replace found data. Supports capture variables and special replacement symbols.
70
71 - Capture Variables: $1 represents the text of the first submatch
72 - {nr} inserts a record number starting from 1
73 - {kv} uses corresponding value of the key (captured variable $n) of a key-value file
74
75 If using the special replacement symbols, the capture variable must be specified as ${1}!
76 ]]>
77 </help>
78 <expand macro="text_sanitizer" />
79 </param>
80 <param name="input_kv" type="data" format="tsv,tabular" argument="-k"
81 optional="true"
82 label="Key/Value file for replacement string"
83 help="Only specify a file if using {kv} in replacement string. The file must be tab delimited with one key/value pair per line.
84 An example can be found in the help section below"
85 />
86 <conditional name="fill">
87 <param name="how_fill" type="select" label="Fill columns that don't get any regex matches">
88 <option value="no">No</option>
89 <option value="key">Yes - Fill with Original Value</option>
90 <option value="string">Yes - Fill with String</option>
91 </param>
92 <when value="no" />
93 <when value="key" />
94 <when value="string" >
95 <param name="fill_string" type="text" value="NA" argument="--key-miss-repl" label="Fill string">
96 <expand macro="text_sanitizer" />
97 </param>
98 </when>
99 </conditional>
100 <expand macro="ignore_case" />
101 <expand macro="global_parameters" />
102 </inputs>
103 <outputs>
104 <data format_source="in_1" name="replaced" from_work_dir="replaced" label='${in_1.name} with column ${column_text.in_text} replaced' />
105 </outputs>
106 <tests>
107 <test>
108 <param name="in_1" value="replace_input.csv" />
109 <conditional name="column_text">
110 <param name="select" value="string" />
111 <param name="in_text" value="2" />
112 </conditional>
113 <param name="pattern_string" value=".+" />
114 <param name="replacement_string" value="{nr}-$1" />
115 <output name="replaced" value="replace_1.csv" />
116 </test>
117 <test>
118 <param name="in_1" value="replace_input.csv" />
119 <conditional name="column_text">
120 <param name="select" value="string" />
121 <param name="in_text" value="2" />
122 </conditional>
123 <param name="pattern_string" value=".+" />
124 <param name="replacement_string" value="{kv}" />
125 <param name="input_kv" value="kv.txt" />
126 <conditional name="fill">
127 <param name="how_fill" value="key" />
128 </conditional>
129 <output name="replaced" value="replace_2.csv" />
130 </test>
131 </tests>
132 <help><![CDATA[
133
134 Csvtk - Replace Help
135 --------------------
136
137 Info
138 ####
139 Csvtk-replace is a tool that uses Regular Expressions (Regex) to match data in the specified column and replace it with the replacement string.
140 Non-matched columns can be kept or filled with the Regex key or an input string
141
142 The regex input for this tool is structured such that your regular expression **does not** need to start with with quotes or brackets. You can
143 start your expression with a `^` or just go straight into it
144
145 For example:
146
147 ::
148
149 Using `.+` as an input would be used in the code as '(.+)'
150
151 Using ^(.+)$ as an input would yield an input in the code as '(^(.+)$)'
152
153 .. class:: warningmark
154
155 Single quotes are not allowed in text inputs!
156
157 -----
158
159
160 @HELP_INPUT_DATA@
161
162
163 Usage
164 #####
165 You can use csvtk replace to any matched regex expressions with your input replacement string.
166
167 The replacement string has some unique properties that you can use too to better replace your data:
168
169 - Replacement supports capture variables, like $1 which represents the text of the first submatch of the Regex
170
171 - \{nr} can be used to assign ascending numbers starting from 1 to each column
172
173 - \{kv} can be used to get the value of the key (captured variable $n) or a key-value file
174
175 A good Regular expressions cheat sheet that you can use to help yourself build regular expressions can be found at:
176 https://regexr.com/
177
178 **Replace Examples**
179
180 1. Replacement with {nr} and $1
181
182 Input file:
183
184 +---------+--------+
185 | Name | Animal |
186 +=========+========+
187 | Bud | Dog |
188 +---------+--------+
189 | Mittens | Cat |
190 +---------+--------+
191
192 Now if our regex was set to '.*' on column 2 and our replacement string was set to '{nr}-$1', the following output would be observed:
193
194 +---------+--------+
195 | Name | Animal |
196 +=========+========+
197 | Bud | 1-Dog |
198 +---------+--------+
199 | Mittens | 2-Cat |
200 +---------+--------+
201
202 ---------------
203
204 2. Replacement with {kv} file
205
206 Suppose you set up a key-value TAB separated file that looked as such:
207
208 ::
209
210 Key Value
211 Dog Big
212 Cat Small
213
214 And had a similar input file:
215
216 +---------+--------+
217 | Name | Animal |
218 +=========+========+
219 | Bud | Dog |
220 +---------+--------+
221 | Mittens | Cat |
222 +---------+--------+
223 | Fuzzy | Gerbil |
224 +---------+--------+
225
226 Now if the regex was '.*' on column 2 with the replacement string as '{kv}'. Your output would look as such with 'No' fill specified:
227
228 +---------+--------+
229 | Name | Animal |
230 +=========+========+
231 | Bud | Big |
232 +---------+--------+
233 | Mittens | Small |
234 +---------+--------+
235 | Fuzzy | |
236 +---------+--------+
237
238 If you wanted to fill the blank cell you could set it to either:
239
240 - String - the string you input (ex. 'NA') would fill up the blank cell.
241
242 - Original value - would change the blank cell to 'Gerbil'
243
244 ----
245
246 If your having trouble with the regular expressions, please play around with a builder, there are many others online
247 and they are great resources to improve your regex statements or test them before use!
248
249 ----
250
251 @HELP_END_STATEMENT@
252
253
254 ]]></help>
255 <expand macro="citations" />
256 </tool>