Mercurial > repos > bgruening > text_processing
annotate grep.xml @ 12:062ed2bb4f2e draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f8896018f5b980a456c4ceaffe0ed457dc80b5a8
| author | bgruening |
|---|---|
| date | Thu, 02 Jun 2016 08:58:39 -0400 |
| parents | c78b1767db2b |
| children | 3c685c4106b3 |
| rev | line source |
|---|---|
| 4 | 1 <tool id="tp_grep_tool" name="Search in textfiles" version="@BASE_VERSION@.0"> |
| 0 | 2 <description>(grep)</description> |
| 4 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"> | |
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062ed2bb4f2e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f8896018f5b980a456c4ceaffe0ed457dc80b5a8
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7 <requirement type="package" version="2.14">grep</requirement> |
| 4 | 8 </expand> |
| 9 <version_command>grep --version | head -n 1</version_command> | |
| 2 | 10 <command> |
| 4 | 11 <![CDATA[ |
| 2 | 12 #if str($color) == "COLOR": |
| 4 | 13 GREP_COLOR='1;34' |
| 14 grep | |
| 15 --color=always | |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
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16 $regex_type |
| 4 | 17 -A $lines_after |
| 18 -B $lines_before | |
| 19 $invert | |
| 20 $case_sensitive | |
| 21 -- "${url_paste}" | |
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fa7f88da29d7
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
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22 '${infile}' | $__tool_directory__/ansi2html.sh > "${output}" |
| 0 | 23 #else: |
| 4 | 24 grep |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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25 $regex_type |
| 4 | 26 -A $lines_after |
| 27 -B $lines_before | |
| 28 $invert | |
| 29 $case_sensitive | |
| 30 -- "${url_paste}" | |
| 31 '${infile}' | grep -v "^--$" > "${output}" | |
| 0 | 32 #end if |
| 33 | |
| 4 | 34 ##grep_wrapper.sh '$infile' '$output' '$url_paste' $color -A $lines_after -B $lines_before $invert $case_sensitive |
| 35 ]]> | |
| 0 | 36 </command> |
| 37 <inputs> | |
| 4 | 38 <param name="infile" format="txt" type="data" label="Select lines from" /> |
| 0 | 39 |
| 40 <param name="invert" type="select" label="that"> | |
| 41 <option value="">Match</option> | |
| 42 <option value="-v">Don't Match</option> | |
| 43 </param> | |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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44 |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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45 <param name="regex_type" type="select" label="Type of regex"> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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46 <option value="-G">Basic</option> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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47 <option value="-P" selected="true">Perl</option> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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48 <option value="-E">Extended (egrep)</option> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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49 </param> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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50 |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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51 <param name="url_paste" type="text" label="Regular Expression" help="See below for more details"> |
| 0 | 52 <sanitizer> |
| 53 <valid initial="string.printable"> | |
| 54 <remove value="'"/> | |
| 55 </valid> | |
| 56 </sanitizer> | |
| 57 </param> | |
| 58 | |
| 4 | 59 <param name="case_sensitive" type="select" label="Match type" help="(-i)"> |
| 0 | 60 <option value="-i">case insensitive</option> |
| 61 <option value="">case sensitive</option> | |
| 62 </param> | |
| 4 | 63 <param name="lines_before" type="integer" value="0" |
| 64 label="Show lines preceding the matched line" help="leave it at zero unless you know what you're doing. (-B)" /> | |
| 65 <param name="lines_after" type="integer" value="0" | |
| 66 label="Show lines trailing the matched line" help="leave it at zero unless you know what you're doing. (-A)" /> | |
| 0 | 67 <param name="color" type="select" label="Output"> |
| 68 <option value="NOCOLOR">text file (for further processing)</option> | |
| 69 <option value="COLOR">Highlighted HTML (for easier viewing)</option> | |
| 70 </param> | |
| 71 | |
| 4 | 72 </inputs> |
| 73 <outputs> | |
| 6 | 74 <data name="output" format_source="infile" metadata_source="infile"> |
| 4 | 75 <change_format> |
| 76 <when input="color" value="COLOR" format="html"/> | |
| 77 </change_format> | |
| 78 </data> | |
| 79 </outputs> | |
| 80 <tests> | |
| 81 <test> | |
| 82 <!-- grep a FASTA file for sequences with specific motif --> | |
| 6 | 83 <param name="infile" value="grep1.txt" /> |
| 4 | 84 <param name="case_sensitive" value="case sensitive" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
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changeset
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85 <param name="regex_type" value="-P" /> |
| 4 | 86 <param name="invert" value="" /> |
| 87 <param name="url_paste" value="AA.{2}GT" /> | |
| 88 <param name="lines_before" value="1" /> | |
| 89 <param name="lines_after" value="0" /> | |
| 90 <param name="color" value="NOCOLOR" /> | |
| 6 | 91 <output name="output" file="grep_results1.txt" /> |
| 4 | 92 </test> |
| 93 <test> | |
| 94 <!-- grep a FASTA file for sequences with specific motif - | |
| 0 | 95 show highlighed output --> |
| 6 | 96 <param name="infile" value="grep1.txt" /> |
| 4 | 97 <param name="case_sensitive" value="case sensitive" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
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changeset
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98 <param name="regex_type" value="-P" /> |
| 4 | 99 <param name="invert" value="" /> |
| 100 <param name="url_paste" value="AA.{2}GT" /> | |
| 101 <param name="lines_before" value="0" /> | |
| 102 <param name="lines_after" value="0" /> | |
| 103 <param name="color" value="COLOR" /> | |
| 6 | 104 <output name="output" file="grep_results2.html" /> |
| 4 | 105 </test> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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106 <test><!-- tests egrep --> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
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changeset
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107 <param name="infile" value="egrep1.txt" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
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changeset
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108 <param name="case_sensitive" value="case sensitive" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
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109 <param name="regex_type" value="-E" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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110 <param name="invert" value="" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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111 <param name="url_paste" value="[^ ]+" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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112 <param name="lines_before" value="0" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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113 <param name="lines_after" value="0" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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114 <param name="color" value="NOCOLOR" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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115 <output name="output" file="egrep_results1.txt" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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116 </test> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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117 <test><!-- same regex as egrep test, but different outcome with basic regex --> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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118 <param name="infile" value="egrep1.txt" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
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119 <param name="case_sensitive" value="case sensitive" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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120 <param name="regex_type" value="-G" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
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121 <param name="invert" value="" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
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122 <param name="url_paste" value="[^ ]+" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
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123 <param name="lines_before" value="0" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
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changeset
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124 <param name="lines_after" value="0" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
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125 <param name="color" value="NOCOLOR" /> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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126 <output name="output" file="egrep_results2.txt" />> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
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127 </test> |
| 4 | 128 </tests> |
| 129 <help> | |
| 130 <![CDATA[ | |
| 0 | 131 **What it does** |
| 132 | |
| 133 This tool runs the unix **grep** command on the selected data file. | |
| 134 | |
| 135 .. class:: infomark | |
| 136 | |
| 137 **TIP:** This tool uses the **perl** regular expression syntax (same as running 'grep -P'). This is **NOT** the POSIX or POSIX-extended syntax (unlike the awk/sed tools). | |
| 138 | |
| 139 | |
| 140 **Further reading** | |
| 141 | |
| 142 - Wikipedia's Regular Expression page (http://en.wikipedia.org/wiki/Regular_expression) | |
| 143 - Regular Expressions cheat-sheet (PDF) (http://www.addedbytes.com/cheat-sheets/download/regular-expressions-cheat-sheet-v2.pdf) | |
| 144 - Grep Tutorial (http://www.panix.com/~elflord/unix/grep.html) | |
| 145 | |
| 146 ----- | |
| 147 | |
| 148 **Grep Examples** | |
| 149 | |
| 150 - **AGC.AAT** would match lines with AGC followed by any character, followed by AAT (e.g. **AGCQAAT**, **AGCPAAT**, **AGCwAAT**) | |
| 151 - **C{2,5}AGC** would match lines with 2 to 5 consecutive Cs followed by AGC | |
| 152 - **TTT.{4,10}AAA** would match lines with 3 Ts, followed by 4 to 10 characters (any characeters), followed by 3 As. | |
| 153 - **^chr([0-9A-Za-z])+** would match lines that begin with chromsomes, such as lines in a BED format file. | |
| 154 - **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively. | |
| 155 - **hsa|mmu** would match lines containing "hsa" or "mmu" (or both). | |
| 7 | 156 |
| 0 | 157 ----- |
| 158 | |
| 159 **Regular Expression Syntax** | |
| 160 | |
| 7 | 161 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. |
| 0 | 162 |
| 163 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. | |
| 164 - **^** matches the beginning of a string(but not an internal line). | |
| 165 - **\\d** matches a digit, same as [0-9]. | |
| 166 - **\\D** matches a non-digit. | |
| 167 - **\\s** matches a whitespace character. | |
| 168 - **\\S** matches anything BUT a whitespace. | |
| 169 - **\\t** matches a tab. | |
| 170 - **\\w** matches an alphanumeric character ( A to Z, 0 to 9 and underscore ) | |
| 171 - **\\W** matches anything but an alphanumeric character. | |
| 172 - **(** .. **)** groups a particular pattern. | |
| 173 - **\\Z** matches the end of a string(but not a internal line). | |
| 174 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. | |
| 175 | |
| 176 - **{n}** The preceding item is matched exactly n times. | |
| 7 | 177 - **{n,}** The preceding item ismatched n or more times. |
| 178 - **{n,m}** The preceding item is matched at least n times but not more than m times. | |
| 0 | 179 |
| 180 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**. | |
| 181 - **.** Matches any single character except a newline. | |
| 182 - ***** The preceding item will be matched zero or more times. | |
| 183 - **?** The preceding item is optional and matched at most once. | |
| 184 - **+** The preceding item will be matched one or more times. | |
| 185 - **^** has two meaning: | |
| 7 | 186 - matches the beginning of a line or string. |
| 0 | 187 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. |
| 188 - **$** matches the end of a line or string. | |
| 7 | 189 - **\|** Separates alternate possibilities. |
| 0 | 190 |
| 4 | 191 @REFERENCES@ |
| 192 ]]> | |
| 193 </help> | |
| 0 | 194 </tool> |