[3] | 1 | <tool id="cshl_find_and_replace" name="Find and Replace"> |
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| 2 | <description>text</description> |
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| 3 | <command interpreter="perl"> |
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| 4 | find_and_replace.pl |
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| 5 | #if $searchwhere.choice == "column": |
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| 6 | -c $searchwhere.column |
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| 7 | #end if |
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| 8 | -o $output |
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| 9 | $caseinsensitive |
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| 10 | $wholewords |
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| 11 | $skip_first_line |
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| 12 | $is_regex |
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| 13 | '$url_paste' |
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| 14 | '$file_data' |
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| 15 | '$input' |
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| 16 | </command> |
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| 17 | <inputs> |
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| 18 | <param format="txt" name="input" type="data" label="File to process" /> |
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| 19 | |
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| 20 | <!-- Note: the parameter ane MUST BE 'url_paste' - |
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| 21 | This is a hack in the galaxy library (see ./lib/galaxy/util/__init__.py line 142) |
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| 22 | If the name is 'url_paste' the string won't be sanitized, and all the non-alphanumeric characters |
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| 23 | will be passed to the shell script --> |
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| 24 | <param name="url_paste" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > |
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| 25 | <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator> |
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| 26 | </param> |
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| 27 | |
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| 28 | <param name="file_data" 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." > |
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| 29 | <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator> |
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| 30 | </param> |
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| 31 | |
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| 32 | <param name="is_regex" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Find-Pattern is a regular expression" |
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| 33 | help="see help section for details." /> |
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| 34 | |
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| 35 | <param name="caseinsensitive" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Case-Insensitive search" |
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| 36 | help="" /> |
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| 37 | |
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| 38 | <param name="wholewords" type="boolean" checked="false" truevalue="-w" falsevalue="" label="find whole-words" |
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| 39 | help="ignore partial matches (e.g. 'apple' will not match 'snapple') " /> |
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| 40 | |
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| 41 | <param name="skip_first_line" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Ignore first line" |
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| 42 | help="Select this option if the first line contains column headers. Text in the line will not be replaced. " /> |
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| 43 | |
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| 44 | <conditional name="searchwhere"> |
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| 45 | <param name="choice" type="select" label="Replace text in"> |
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| 46 | <option value="line" selected="true">entire line</option> |
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| 47 | <option value="column">specific column</option> |
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| 48 | </param> |
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| 49 | |
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| 50 | <when value="line"> |
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| 51 | </when> |
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| 52 | |
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| 53 | <when value="column"> |
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| 54 | <param name="column" label="in column" type="data_column" data_ref="input" accept_default="true" /> |
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| 55 | </when> |
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| 56 | </conditional> |
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| 57 | </inputs> |
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| 58 | |
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| 59 | <outputs> |
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| 60 | <data format="input" name="output" metadata_source="input" /> |
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| 61 | </outputs> |
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| 62 | |
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| 63 | <help> |
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| 64 | |
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| 65 | **What it does** |
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| 66 | |
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| 67 | This tool finds & replaces text in an input dataset. |
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| 68 | |
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| 69 | .. class:: infomark |
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| 70 | |
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| 71 | The **pattern to find** can be a simple text string, or a perl **regular expression** string (depending on *pattern is a regex* check-box). |
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| 72 | |
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| 73 | .. class:: infomark |
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| 74 | |
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| 75 | When using regular expressions, the **replace pattern** can contain back-references ( e.g. \\1 ) |
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| 76 | |
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| 77 | .. class:: infomark |
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| 78 | |
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| 79 | This tool uses Perl regular expression syntax. |
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| 80 | |
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| 81 | ----- |
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| 82 | |
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| 83 | **Examples of *regular-expression* Find Patterns** |
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| 84 | |
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| 85 | - **HELLO** The word 'HELLO' (case sensitive). |
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| 86 | - **AG.T** The letters A,G followed by any single character, followed by the letter T. |
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| 87 | - **A{4,}** Four or more consecutive A's. |
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| 88 | - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character. |
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| 89 | - **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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| 90 | |
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| 91 | |
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| 92 | **Examples of Replace Patterns** |
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| 93 | |
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| 94 | - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found. |
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| 95 | - **FOO-&-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **&** (ampersand) represents the matched find pattern. |
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| 96 | - **\\1** The text which matched the first parenthesis in the Find Pattern. |
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| 97 | |
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| 98 | |
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| 99 | ----- |
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| 100 | |
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| 101 | **Example 1** |
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| 102 | |
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| 103 | **Find Pattern:** HELLO |
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| 104 | **Replace Pattern:** WORLD |
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| 105 | **Regular Expression:** no |
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| 106 | **Replace what:** entire line |
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| 107 | |
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| 108 | Every time the word HELLO is found, it will be replaced with the word WORLD. |
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| 109 | |
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| 110 | ----- |
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| 111 | |
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| 112 | **Example 2** |
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| 113 | |
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| 114 | **Find Pattern:** ^chr |
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| 115 | **Replace Pattern:** (empty) |
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| 116 | **Regular Expression:** yes |
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| 117 | **Replace what:** column 11 |
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| 118 | |
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| 119 | If column 11 (of every line) begins with ther letters 'chr', they will be removed. Effectively, it'll turn "chr4" into "4" and "chrXHet" into "XHet" |
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| 120 | |
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| 121 | |
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| 122 | ----- |
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| 123 | |
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| 124 | **Perl's Regular Expression Syntax** |
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| 125 | |
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| 126 | The Find & Replace 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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| 127 | |
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| 128 | - **( ) { } [ ] . * ? + \\ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. |
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| 129 | - **^** matches the beginning of a string(but not an internal line). |
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| 130 | - **(** .. **)** groups a particular pattern. |
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| 131 | - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. |
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| 132 | |
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| 133 | - **{n}** The preceding item is matched exactly n times. |
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| 134 | - **{n,}** The preceding item ismatched n or more times. |
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| 135 | - **{n,m}** The preceding item is matched at least n times but not more than m times. |
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| 136 | |
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| 137 | - **[** ... **]** 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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| 138 | - **.** Matches any single character except a newline. |
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| 139 | - ***** The preceding item will be matched zero or more times. |
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| 140 | - **?** The preceding item is optional and matched at most once. |
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| 141 | - **+** The preceding item will be matched one or more times. |
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| 142 | - **^** has two meaning: |
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| 143 | - matches the beginning of a line or string. |
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| 144 | - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. |
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| 145 | - **$** matches the end of a line or string. |
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| 146 | - **\\|** Separates alternate possibilities. |
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| 147 | - **\\d** matches a single digit |
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| 148 | - **\\w** matches a single letter or digit or an underscore. |
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| 149 | - **\\s** matches a single white-space (space or tabs). |
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| 150 | |
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| 151 | |
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| 152 | </help> |
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| 153 | |
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| 154 | </tool> |
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