Mercurial > repos > bgruening > text_processing
annotate find_and_replace.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_find_and_replace" name="Replace" version="@BASE_VERSION@.0"> |
| 2 | 2 <description>parts of text</description> |
| 4 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 0 | 6 <command interpreter="perl"> |
| 4 | 7 <![CDATA[ |
| 0 | 8 find_and_replace |
| 4 | 9 #if $searchwhere.searchwhere_select == "column": |
| 0 | 10 -c $searchwhere.column |
| 11 #end if | |
| 4 | 12 -o $outfile |
| 0 | 13 $caseinsensitive |
| 14 $wholewords | |
| 15 $skip_first_line | |
| 16 $is_regex | |
| 4 | 17 '$find_pattern' |
| 18 '$replace_pattern' | |
| 19 '$infile' | |
| 20 ]]> | |
| 0 | 21 </command> |
| 22 <inputs> | |
| 4 | 23 <param name="infile" format="txt" type="data" label="File to process" /> |
|
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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:
7
diff
changeset
|
24 <param name="find_pattern" type="text" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > |
| 0 | 25 <sanitizer> |
| 26 <valid initial="string.printable"> | |
| 27 <remove value="'"/> | |
| 28 </valid> | |
| 29 </sanitizer> | |
| 30 </param> | |
|
10
c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
7
diff
changeset
|
31 <param name="replace_pattern" type="text" label="Replace with" |
| 6 | 32 help="Use simple text, or $& (dollar-ampersand) and $1 $2 $3 to refer to matched text. See examples below." > |
| 0 | 33 <sanitizer> |
| 34 <valid initial="string.printable"> | |
| 35 <remove value="'"/> | |
| 36 </valid> | |
| 37 </sanitizer> | |
| 38 </param> | |
| 4 | 39 <param name="is_regex" type="boolean" checked="false" truevalue="-r" falsevalue="" |
| 40 label="Find-Pattern is a regular expression" help="see help section for details." /> | |
| 0 | 41 |
| 4 | 42 <param name="caseinsensitive" type="boolean" checked="false" truevalue="-i" falsevalue="" |
| 43 label="Case-Insensitive search" help="" /> | |
| 0 | 44 |
| 4 | 45 <param name="wholewords" type="boolean" checked="false" truevalue="-w" falsevalue="" |
| 46 label="Find whole-words" help="ignore partial matches (e.g. 'apple' will not match 'snapple')" /> | |
| 0 | 47 |
| 4 | 48 <param name="skip_first_line" type="boolean" checked="false" truevalue="-s" falsevalue="" |
| 49 label="Ignore first line" help="Select this option if the first line contains column headers. Text in the line will not be replaced. " /> | |
| 0 | 50 |
| 51 <conditional name="searchwhere"> | |
| 4 | 52 <param name="searchwhere_select" type="select" label="Find and Replace text in"> |
| 0 | 53 <option value="line" selected="true">entire line</option> |
| 54 <option value="column">specific column</option> | |
| 55 </param> | |
| 56 <when value="line" /> | |
| 57 <when value="column"> | |
| 4 | 58 <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" /> |
| 0 | 59 </when> |
| 60 </conditional> | |
| 61 </inputs> | |
| 62 <outputs> | |
| 6 | 63 <data format_source="infile" name="outfile" metadata_source="infile" /> |
| 0 | 64 </outputs> |
| 4 | 65 <tests> |
| 66 <test> | |
| 67 <param name="infile" value="find_and_replace1.txt" /> | |
| 68 <param name="find_pattern" value="day" /> | |
| 69 <param name="replace_pattern" value="great day" /> | |
| 70 <param name="is_regex" value="False" /> | |
| 71 <param name="caseinsensitive" value="False" /> | |
| 72 <param name="wholewords" value="True" /> | |
| 73 <output name="outfile" file="find_and_replace_results1.txt" /> | |
| 74 </test> | |
| 75 <test> | |
| 76 <param name="infile" value="find_and_replace2.txt" /> | |
| 77 <param name="find_pattern" value="^chr" /> | |
| 78 <param name="replace_pattern" value="" /> | |
| 79 <param name="is_regex" value="True" /> | |
| 80 <param name="caseinsensitive" value="False" /> | |
| 81 <param name="wholewords" value="False" /> | |
| 82 <param name="searchwhere_select" value="column" /> | |
| 83 <param name="column" value="3" /> | |
| 84 <output name="outfile" file="find_and_replace_results2.txt" /> | |
| 85 </test> | |
| 86 </tests> | |
| 87 <help> | |
| 88 <![CDATA[ | |
| 0 | 89 **What it does** |
| 90 | |
| 4 | 91 This tool finds $ replaces text in an input dataset. |
| 0 | 92 |
| 93 .. class:: infomark | |
| 94 | |
| 95 The **pattern to find** can be a simple text string, or a perl **regular expression** string (depending on *pattern is a regex* check-box). | |
| 96 | |
| 97 .. class:: infomark | |
| 98 | |
| 99 When using regular expressions, the **replace pattern** can contain back-references ( e.g. \\1 ) | |
| 100 | |
| 101 .. class:: infomark | |
| 102 | |
| 103 This tool uses Perl regular expression syntax. | |
| 104 | |
| 105 ----- | |
| 106 | |
| 107 **Examples of *regular-expression* Find Patterns** | |
| 108 | |
| 109 - **HELLO** The word 'HELLO' (case sensitive). | |
| 110 - **AG.T** The letters A,G followed by any single character, followed by the letter T. | |
| 111 - **A{4,}** Four or more consecutive A's. | |
| 112 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character. | |
| 113 - **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. | |
| 114 | |
| 115 | |
| 116 **Examples of Replace Patterns** | |
| 117 | |
| 118 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found. | |
| 6 | 119 - **FOO-$&-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **$&** (dollar-ampersand) represents the matched find pattern. |
| 0 | 120 - **$1** The text which matched the first parenthesis in the Find Pattern. |
| 121 | |
| 122 | |
| 123 ----- | |
| 124 | |
| 125 **Example 1** | |
| 126 | |
| 127 **Find Pattern:** HELLO | |
| 128 **Replace Pattern:** WORLD | |
| 129 **Regular Expression:** no | |
| 130 **Replace what:** entire line | |
| 131 | |
| 4 | 132 Every time the word HELLO is found, it will be replaced with the word WORLD. |
| 0 | 133 |
| 134 ----- | |
| 135 | |
| 136 **Example 2** | |
| 137 | |
| 7 | 138 **Find Pattern:** ^chr |
| 0 | 139 **Replace Pattern:** (empty) |
| 140 **Regular Expression:** yes | |
| 141 **Replace what:** column 11 | |
| 142 | |
| 143 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" | |
| 144 | |
| 145 | |
| 146 ----- | |
| 147 | |
| 148 **Perl's Regular Expression Syntax** | |
| 149 | |
| 7 | 150 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. |
| 0 | 151 |
| 152 - **( ) { } [ ] . * ? + \\ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. | |
| 153 - **^** matches the beginning of a string(but not an internal line). | |
| 154 - **(** .. **)** groups a particular pattern. | |
| 155 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. | |
| 156 | |
| 157 - **{n}** The preceding item is matched exactly n times. | |
| 7 | 158 - **{n,}** The preceding item ismatched n or more times. |
| 159 - **{n,m}** The preceding item is matched at least n times but not more than m times. | |
| 0 | 160 |
| 161 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**. | |
| 162 - **.** Matches any single character except a newline. | |
| 163 - ***** The preceding item will be matched zero or more times. | |
| 164 - **?** The preceding item is optional and matched at most once. | |
| 165 - **+** The preceding item will be matched one or more times. | |
| 166 - **^** has two meaning: | |
| 7 | 167 - matches the beginning of a line or string. |
| 0 | 168 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. |
| 169 - **$** matches the end of a line or string. | |
| 7 | 170 - **\\|** Separates alternate possibilities. |
| 0 | 171 - **\\d** matches a single digit |
| 172 - **\\w** matches a single letter or digit or an underscore. | |
| 173 - **\\s** matches a single white-space (space or tabs). | |
| 174 | |
| 4 | 175 @REFERENCES@ |
| 176 ]]> | |
| 177 </help> | |
| 0 | 178 </tool> |