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comparison replace_text_in_column.xml @ 4:56e80527c482 draft

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author bgruening
date Wed, 07 Jan 2015 11:10:52 -0500
parents 7068d1548234
children 8928e6d1e7ba
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3:7068d1548234 4:56e80527c482
1 <tool id="tp_replace_in_column" name="Replace Text" version="0.1"> 1 <tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.0">
2 <description>in a specific column</description> 2 <description>in a specific column</description>
3 <requirements> 3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
4 <requirement type="package" version="4.1.0">gnu_awk</requirement> 7 <requirement type="package" version="4.1.0">gnu_awk</requirement>
5 </requirements> 8 </expand>
9 <version_command>awk --version | head -n 1</version_command>
6 <command interpreter="sh"> 10 <command interpreter="sh">
7 #adapt to awk's quirks - to pass an acutal backslash - two backslashes are required (just like in a C string) 11 <![CDATA[
12 ##adapt to awk's quirks - to pass an acutal backslash - two backslashes are required (just like in a C string)
8 REPLACE_PATTERN=\${$replace_pattern//\\/\\\\}; 13 REPLACE_PATTERN=\${$replace_pattern//\\/\\\\};
9 awk -v OFS="\t" --re-interval --sandbox "{ \$$column = gensub( /$find_pattern/, \"$replace_pattern\", \"g\", \$$column ) ; print \$0 ; }" "$input" &gt; "$output" 14 awk
15 -v OFS="\t"
16 --re-interval
17 --sandbox "{ \$$column = gensub( /$find_pattern/, \"$replace_pattern\", \"g\", \$$column ) ; print \$0 ; }"
18 "$infile"
19 > "$output"
20 ]]>
10 </command> 21 </command>
11 <inputs> 22 <inputs>
12 <param format="tabular" name="input" type="data" label="File to process" /> 23 <param format="tabular" name="infile" type="data" label="File to process" />
13 <param name="column" label="in column" type="data_column" data_ref="input" accept_default="true" /> 24 <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" />
14 25
15 <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > 26 <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
16 <sanitizer> 27 <sanitizer>
17 <valid initial="string.printable"> 28 <valid initial="string.printable">
18 <remove value="&apos;"/> 29 <remove value="&apos;"/>
19 </valid> 30 </valid>
20 </sanitizer> 31 </sanitizer>
21 </param> 32 </param>
22
23 <param name="replace_pattern" type="text" size="20" label="Replace with" help="Use simple text, or &amp; (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." > 33 <param name="replace_pattern" type="text" size="20" label="Replace with" help="Use simple text, or &amp; (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." >
24 <sanitizer> 34 <sanitizer>
25 <valid initial="string.printable"> 35 <valid initial="string.printable">
26 <remove value="&apos;"/> 36 <remove value="&apos;"/>
27 </valid> 37 </valid>
28 </sanitizer> 38 </sanitizer>
29 </param> 39 </param>
30
31 </inputs> 40 </inputs>
41 <outputs>
42 <data format="input" name="output" metadata_source="infile" />
43 </outputs>
32 <tests> 44 <tests>
33 <test> 45 <test>
34 <param name="input" value="replace_text_in_column_in1.txt" ftype="tabular" /> 46 <param name="infile" value="replace_text_in_column_in1.txt" ftype="tabular" />
47 <param name="column" value="4" />
48 <param name="find_pattern" value=".+_(R.)" />
49 <param name="replace_pattern" value="\1" />
35 <output name="output" file="replace_text_in_column_output1.txt" /> 50 <output name="output" file="replace_text_in_column_output1.txt" />
36 <param name="column" value="4" />
37 <param name="url_paste" value=".+_(R.)" />
38 <param name="file_data" value="\1" />
39 </test> 51 </test>
40 </tests> 52 </tests>
41 <outputs>
42 <data format="input" name="output" metadata_source="input" />
43 </outputs>
44 <help> 53 <help>
45 54 <![CDATA[
46 **What it does** 55 **What it does**
47 56
48 This tool performs find &amp; replace operation on a specified column in a given file. 57 This tool performs find &amp; replace operation on a specified column in a given file.
49 58
50 .. class:: infomark 59 .. class:: infomark
70 **Examples of Replace Patterns** 79 **Examples of Replace Patterns**
71 80
72 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found. 81 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found.
73 - **FOO-&amp;-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **&amp;** (ampersand) represents the matched find pattern. 82 - **FOO-&amp;-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **&amp;** (ampersand) represents the matched find pattern.
74 - **\\1** The text which matched the first parenthesis in the Find Pattern. 83 - **\\1** The text which matched the first parenthesis in the Find Pattern.
75
76
77 84
78 85
79 ----- 86 -----
80 87
81 **Example 1** 88 **Example 1**
122 - **\|** Separates alternate possibilities. 129 - **\|** Separates alternate possibilities.
123 130
124 131
125 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. 132 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.
126 133
134 @REFERENCES@
135 ]]>
127 </help> 136 </help>
128 </tool> 137 </tool>