Mercurial > repos > bgruening > text_processing
annotate replace_text_in_line.xml @ 10:c78b1767db2b draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
| author | bgruening |
|---|---|
| date | Fri, 26 Feb 2016 12:22:54 -0500 |
| parents | d64eace4f9f3 |
| children | 062ed2bb4f2e |
| rev | line source |
|---|---|
| 4 | 1 <tool id="tp_replace_in_line" name="Replace Text" version="@BASE_VERSION@.0"> |
| 3 | 2 <description>in entire line</description> |
| 4 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"> | |
| 3 | 7 <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement> |
| 4 | 8 </expand> |
| 9 <version_command>sed --version | head -n 1</version_command> | |
| 6 | 10 <command> |
| 4 | 11 <![CDATA[ |
| 7 | 12 sed |
| 4 | 13 -r |
| 14 --sandbox | |
| 15 "s/$find_pattern/$replace_pattern/g" | |
| 6 | 16 "$infile" |
| 17 > "$outfile" | |
| 4 | 18 ]]> |
| 3 | 19 </command> |
| 20 <inputs> | |
| 6 | 21 <param format="txt" name="infile" type="data" label="File to process" /> |
|
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
|
22 <param name="find_pattern" type="text" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > |
| 3 | 23 <sanitizer> |
| 24 <valid initial="string.printable"> | |
| 25 <remove value="'"/> | |
| 26 </valid> | |
| 27 </sanitizer> | |
| 28 </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
|
29 <param name="replace_pattern" type="text" label="Replace with:" help="Use simple text, or & (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." > |
| 3 | 30 <sanitizer> |
| 31 <valid initial="string.printable"> | |
| 32 <remove value="'"/> | |
| 33 </valid> | |
| 34 </sanitizer> | |
| 35 </param> | |
| 36 </inputs> | |
| 37 <outputs> | |
| 6 | 38 <data name="outfile" format_source="infile" metadata_source="infile"/> |
| 3 | 39 </outputs> |
| 4 | 40 <tests> |
| 41 <test> | |
| 6 | 42 <param name="infile" value="replace_text_in_line1.txt" /> |
| 4 | 43 <param name="find_pattern" value="CTC." /> |
| 44 <param name="replace_pattern" value="FOOBAR" /> | |
| 6 | 45 <output name="outfile" file="replace_text_in_line_results1.txt" /> |
| 4 | 46 </test> |
| 47 </tests> | |
| 3 | 48 <help> |
| 4 | 49 <![CDATA[ |
| 3 | 50 **What it does** |
| 51 | |
| 6 | 52 This tool performs find & replace operation on a specified file. |
| 3 | 53 |
| 54 .. class:: infomark | |
| 55 | |
| 56 The **pattern to find** uses the **extended regular** expression syntax (same as running 'sed -r'). | |
| 57 | |
| 58 .. class:: infomark | |
| 59 | |
| 60 **TIP:** If you need more complex patterns, use the *sed* tool. | |
| 61 | |
| 62 ----- | |
| 63 | |
| 64 **Examples of Find Patterns** | |
| 65 | |
| 66 - **HELLO** The word 'HELLO' (case sensitive). | |
| 67 - **AG.T** The letters A,G followed by any single character, followed by the letter T. | |
| 68 - **A{4,}** Four or more consecutive A's. | |
| 69 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character. | |
| 70 - **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. | |
| 71 | |
| 72 | |
| 73 **Examples of Replace Patterns** | |
| 74 | |
| 75 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found. | |
| 6 | 76 - **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. |
| 3 | 77 - **\\1** The text which matched the first parenthesis in the Find Pattern. |
| 78 | |
| 79 | |
| 80 ----- | |
| 81 | |
| 82 **Example 1** | |
| 83 | |
| 84 **Find Pattern:** HELLO | |
| 85 **Replace Pattern:** WORLD | |
| 86 | |
| 87 Every time the word HELLO is found, it will be replaced with the word WORLD. | |
| 88 | |
| 89 | |
| 90 ----- | |
| 91 | |
| 92 **Example 2** | |
| 93 | |
| 7 | 94 **Find Pattern:** ^(.{4}) |
| 6 | 95 **Replace Pattern:** &\\t |
| 3 | 96 |
| 97 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. | |
| 98 | |
| 99 | |
| 100 ----- | |
| 101 | |
| 102 **Extened Regular Expression Syntax** | |
| 103 | |
| 7 | 104 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. |
| 3 | 105 |
| 106 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. | |
| 107 - **^** matches the beginning of a string(but not an internal line). | |
| 108 - **(** .. **)** groups a particular pattern. | |
| 109 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. | |
| 110 | |
| 111 - **{n}** The preceding item is matched exactly n times. | |
| 7 | 112 - **{n,}** The preceding item ismatched n or more times. |
| 113 - **{n,m}** The preceding item is matched at least n times but not more than m times. | |
| 3 | 114 |
| 115 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**. | |
| 116 - **.** Matches any single character except a newline. | |
| 117 - ***** The preceding item will be matched zero or more times. | |
| 118 - **?** The preceding item is optional and matched at most once. | |
| 119 - **+** The preceding item will be matched one or more times. | |
| 120 - **^** has two meaning: | |
| 7 | 121 - matches the beginning of a line or string. |
| 3 | 122 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. |
| 123 - **$** matches the end of a line or string. | |
| 7 | 124 - **\|** Separates alternate possibilities. |
| 3 | 125 |
| 126 | |
| 127 **Note**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. | |
| 128 | |
| 4 | 129 @REFERENCES@ |
| 130 ]]> | |
| 3 | 131 </help> |
| 132 </tool> |