Mercurial > repos > bgruening > text_processing
annotate replace_text_in_line.xml @ 14:fb4ff3c42cd3 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 09b22cceacb34dd4c6c1b42890f93232df128208"
author | bgruening |
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date | Sat, 21 Mar 2020 13:49:11 -0400 |
parents | a6f147a050a2 |
children | 12615d397df7 |
rev | line source |
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a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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1 <tool id="tp_replace_in_line" name="Replace Text" version="@BASE_VERSION@.2"> |
0 | 2 <description>in entire line</description> |
3 <macros> | |
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a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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4 <import>macros.xml</import> |
0 | 5 </macros> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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6 <requirements> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7
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7 <requirement type="package" version="4.4">sed</requirement> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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8 </requirements> |
0 | 9 <version_command>sed --version | head -n 1</version_command> |
10 <command> | |
11 <![CDATA[ | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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12 sed |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7
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13 -r |
74a8bef53a00
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7
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14 --sandbox |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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15 #for $replacement in $replacements: |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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16 -e |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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17 's/$replacement.find_pattern/$replacement.replace_pattern/g' |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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18 #end for |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7
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19 '$infile' |
74a8bef53a00
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7
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20 > '$outfile' |
0 | 21 ]]> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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22 |
0 | 23 </command> |
24 <inputs> | |
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a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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25 <param format="txt" name="infile" type="data" label="File to process" /> |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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26 <repeat name="replacements" title="Replacement" min="1"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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27 <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > |
0 | 28 <sanitizer> |
29 <valid initial="string.printable"> | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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30 <remove value="'"/> |
e39fceb6ab85
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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31 <remove value="/"/> |
0 | 32 </valid> |
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e39fceb6ab85
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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33 <mapping initial="none"> |
e39fceb6ab85
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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34 <add source="'" target="'"'"'" /> |
e39fceb6ab85
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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35 <add source="/" target="\/"/> |
e39fceb6ab85
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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36 </mapping> |
0 | 37 </sanitizer> |
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a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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38 </param> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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39 <param name="replace_pattern" type="text" size="20" label="Replace with:" help="Use simple text, or & (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." > |
0 | 40 <sanitizer> |
41 <valid initial="string.printable"> | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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42 <remove value="'"/> |
e39fceb6ab85
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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43 <remove value="/"/> |
0 | 44 </valid> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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45 <mapping initial="none"> |
e39fceb6ab85
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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46 <add source="'" target="'"'"'" /> |
e39fceb6ab85
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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47 <add source="/" target="\/"/> |
e39fceb6ab85
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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48 </mapping> |
e39fceb6ab85
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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49 |
0 | 50 </sanitizer> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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51 |
0 | 52 </param> |
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a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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53 </repeat> |
0 | 54 </inputs> |
55 <outputs> | |
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a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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56 <data name="outfile" format_source="infile" metadata_source="infile"/> |
0 | 57 </outputs> |
58 <tests> | |
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a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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59 <test> |
0 | 60 <param name="infile" value="replace_text_in_line1.txt" /> |
61 <param name="find_pattern" value="CTC." /> | |
62 <param name="replace_pattern" value="FOOBAR" /> | |
63 <output name="outfile" file="replace_text_in_line_results1.txt" /> | |
64 </test> | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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65 <test> |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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66 <param name="infile" value="replace_text_in_line1.txt" /> |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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67 <repeat name="replacements"> |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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68 <param name="find_pattern" value="CTC." /> |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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69 <param name="replace_pattern" value="FOOBAR" /> |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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70 </repeat> |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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71 <repeat name="replacements"> |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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72 <param name="find_pattern" value="chr" /> |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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73 <param name="replace_pattern" value="domain" /> |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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74 </repeat> |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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75 <output name="outfile" file="replace_text_in_line_results2.txt" /> |
a6f147a050a2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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76 </test> |
0 | 77 </tests> |
78 <help> | |
79 <![CDATA[ | |
80 **What it does** | |
81 | |
82 This tool performs find & replace operation on a specified file. | |
83 | |
84 .. class:: infomark | |
85 | |
86 The **pattern to find** uses the **extended regular** expression syntax (same as running 'sed -r'). | |
87 | |
88 .. class:: infomark | |
89 | |
90 **TIP:** If you need more complex patterns, use the *sed* tool. | |
91 | |
92 ----- | |
93 | |
94 **Examples of Find Patterns** | |
95 | |
96 - **HELLO** The word 'HELLO' (case sensitive). | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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97 - **AG.T** The letters A,G followed by any single character, followed by the letter T. |
0 | 98 - **A{4,}** Four or more consecutive A's. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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99 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character. |
0 | 100 - **hsa-mir-([^ ]+)** The text 'hsa-mir-' followed by one-or-more non-space characters. When using parenthesis, the matched content of the parenthesis can be accessed with **\1** in the **replace** pattern. |
101 | |
102 | |
103 **Examples of Replace Patterns** | |
104 | |
105 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found. | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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106 - **FOO-&-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the beginning and '-BAR' at the end. **&** (ampersand) represents the matched find pattern. |
0 | 107 - **\\1** The text which matched the first parenthesis in the Find Pattern. |
108 | |
109 | |
110 ----- | |
111 | |
112 **Example 1** | |
113 | |
114 **Find Pattern:** HELLO | |
115 **Replace Pattern:** WORLD | |
116 | |
117 Every time the word HELLO is found, it will be replaced with the word WORLD. | |
118 | |
119 | |
120 ----- | |
121 | |
122 **Example 2** | |
123 | |
124 **Find Pattern:** ^(.{4}) | |
125 **Replace Pattern:** &\\t | |
126 | |
127 Find the first four characters in each line, and replace them with the same text, followed by a tab character. In practice - this will split the first line into two columns. | |
128 | |
129 | |
130 ----- | |
131 | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
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132 **Extended Regular Expression Syntax** |
0 | 133 |
134 The select tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text. | |
135 | |
136 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. | |
137 - **^** matches the beginning of a string(but not an internal line). | |
138 - **(** .. **)** groups a particular pattern. | |
139 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. | |
140 | |
141 - **{n}** The preceding item is matched exactly n times. | |
142 - **{n,}** The preceding item ismatched n or more times. | |
143 - **{n,m}** The preceding item is matched at least n times but not more than m times. | |
144 | |
145 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**. | |
146 - **.** Matches any single character except a newline. | |
147 - ***** The preceding item will be matched zero or more times. | |
148 - **?** The preceding item is optional and matched at most once. | |
149 - **+** The preceding item will be matched one or more times. | |
150 - **^** has two meaning: | |
151 - matches the beginning of a line or string. | |
152 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. | |
153 - **$** matches the end of a line or string. | |
154 - **\|** Separates alternate possibilities. | |
155 | |
156 | |
157 **Note**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. | |
158 | |
159 @REFERENCES@ | |
160 ]]> | |
161 </help> | |
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162 <expand macro="citations" /> |
0 | 163 </tool> |