Mercurial > repos > bgruening > text_processing

annotate replace_text_in_line.xml @ 27:08cdbfffce67 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
author bgruening
date Fri, 07 Mar 2025 20:43:41 +0000
parents f22a309187a3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
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1 <tool id="tp_replace_in_line" name="Replace Text" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>in entire line</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="creator"/>
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7 <requirements>
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8 <requirement type="package" version="4.8">sed</requirement>
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9 </requirements>
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10 <version_command>sed --version | head -n 1</version_command>
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11 <command>
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12 <![CDATA[
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13 sed
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14 -r
1e974b82380d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7
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15 --sandbox
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16 #for $replacement in $replacements:
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17 -e '$replacement.sed_options'
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18 -e
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321
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19 's/$replacement.find_pattern/$replacement.replace_pattern/g'
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321
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20 #end for
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21 '$infile'
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22 > '$outfile'
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23 ]]>
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24
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25 </command>
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26 <inputs>
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27 <param format="txt" name="infile" type="data" label="File to process" />
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321
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28 <repeat name="replacements" title="Replacement" min="1">
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29 <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
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30 <sanitizer>
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31 <valid initial="string.printable">
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32 <remove value="&#39;"/>
f2918761eaf3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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33 <remove value="/"/>
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34 </valid>
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35 <mapping initial="none">
f2918761eaf3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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36 <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
f2918761eaf3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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37 <add source="/" target="\/"/>
f2918761eaf3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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38 </mapping>
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39 </sanitizer>
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40 </param>
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41 <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." >
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42 <sanitizer>
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43 <valid initial="string.printable">
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44 <remove value="&#39;"/>
f2918761eaf3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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45 <remove value="/"/>
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46 </valid>
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47 <mapping initial="none">
f2918761eaf3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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48 <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
f2918761eaf3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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49 <add source="/" target="\/"/>
f2918761eaf3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
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50 </mapping>
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51 </sanitizer>
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52 </param>
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53 <param name="sed_options" type="text" size="20" optional="true" label="Additional sed commands before replacement" help="Provide additional sed commands before the replacement (e.g., ':a;N;$!ba;')." >
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54 <sanitizer>
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55 <valid initial="string.printable">
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56 <remove value="&#39;"/> <!-- Removes single quotes -->
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57 <remove value="/"/> <!-- Removes slashes -->
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58 </valid>
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59 <mapping initial="none">
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60 <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" /> <!-- Escapes single quotes -->
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61 <add source="/" target="\/"/> <!-- Escapes slashes -->
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62 </mapping>
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63 </sanitizer>
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64 </param>
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65 </repeat>
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66 </inputs>
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67 <outputs>
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68 <data name="outfile" format_source="infile" metadata_source="infile"/>
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69 </outputs>
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70 <tests>
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71 <test>
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72 <param name="infile" value="replace_text_in_line1.txt" />
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73 <repeat name="replacements">
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74 <param name="find_pattern" value="CTC." />
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75 <param name="replace_pattern" value="FOOBAR" />
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76 <param name="sed_options" value="" />
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77 </repeat>
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78 <output name="outfile" file="replace_text_in_line_results1.txt" />
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79 </test>
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80 <test>
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81 <param name="infile" value="replace_text_in_line1.txt" />
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82 <repeat name="replacements">
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83 <param name="find_pattern" value="CTC." />
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84 <param name="replace_pattern" value="FOOBAR" />
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85 <param name="sed_options" value="" />
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86 </repeat>
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87 <repeat name="replacements">
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88 <param name="find_pattern" value="chr" />
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89 <param name="replace_pattern" value="domain" />
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90 <param name="sed_options" value="" />
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91 </repeat>
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92 <output name="outfile" file="replace_text_in_line_results2.txt" />
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93 </test>
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94 <test>
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95 <param name="infile" value="replace_text_in_line1.txt" />
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96 <repeat name="replacements">
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97 <param name="find_pattern" value="\n" />
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98 <param name="replace_pattern" value="" />
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99 <param name="sed_options" value=":a;N;$!ba" />
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100 </repeat>
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101 <output name="outfile" file="replace_text_in_line_results3.txt" />
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102 </test>
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103 </tests>
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104 <help>
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105 <![CDATA[
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106 **What it does**
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107
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108 This tool performs find & replace operation on a specified file.
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109
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110 .. class:: infomark
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111
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112 The **pattern to find** uses the **extended regular** expression syntax (same as running 'sed -r').
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113
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114 .. class:: infomark
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115
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116 **TIP:** If you need more complex patterns, use the *sed* tool.
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117
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118 -----
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119
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120 **Examples of Find Patterns**
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121
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122 - **HELLO** The word 'HELLO' (case sensitive).
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123 - **AG.T** The letters A,G followed by any single character, followed by the letter T.
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124 - **A{4,}** Four or more consecutive A's.
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125 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
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126 - **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.
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127
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128
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129 **Examples of Replace Patterns**
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130
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131 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found.
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132 - **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.
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133 - **\\1** The text which matched the first parenthesis in the Find Pattern.
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134
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135
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136 -----
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137
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138 **Example 1**
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139
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140 **Find Pattern:** HELLO
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141 **Replace Pattern:** WORLD
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142
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143 Every time the word HELLO is found, it will be replaced with the word WORLD.
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144
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145
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146 -----
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147
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148 **Example 2**
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149
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150 **Find Pattern:** ^(.{4})
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151 **Replace Pattern:** &\\t
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152
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153 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.
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154
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155
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156 -----
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157
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158 **Extended Regular Expression Syntax**
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159
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160 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.
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161
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162 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
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163 - **^** matches the beginning of a string(but not an internal line).
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164 - **(** .. **)** groups a particular pattern.
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165 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
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166
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167 - **{n}** The preceding item is matched exactly n times.
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168 - **{n,}** The preceding item ismatched n or more times.
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169 - **{n,m}** The preceding item is matched at least n times but not more than m times.
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170
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171 - **[** ... **]** 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**.
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172 - **.** Matches any single character except a newline.
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173 - ***** The preceding item will be matched zero or more times.
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174 - **?** The preceding item is optional and matched at most once.
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175 - **+** The preceding item will be matched one or more times.
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176 - **^** has two meaning:
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177 - matches the beginning of a line or string.
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178 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
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179 - **$** matches the end of a line or string.
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180 - **\|** Separates alternate possibilities.
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181
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182
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183 **Note**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. However, you can use SED FAQ to perform commands using special characters.
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184 More complex options can look like `sed -e '$!N;s/foo/bar/;'`. Here, `$!N;` is an optional part which you only need to set in very special cases. The `foo` part is the search string, and the `bar` part is the replacement string.
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185 Please read the SED FAQ here: https://www.pement.org/sed/sedfaq3.html#s3.2
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186
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187 ]]>
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188 </help>
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189 <expand macro="citations" />
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190 </tool>