Mercurial > repos > bgruening > text_processing
annotate replace_text_in_column.xml @ 11:e6d48dc4e6ba draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
| author | bgruening |
|---|---|
| date | Fri, 18 Mar 2016 15:18:21 -0400 |
| parents | c78b1767db2b |
| children | 062ed2bb4f2e |
| rev | line source |
|---|---|
| 4 | 1 <tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.0"> |
| 3 | 2 <description>in a specific column</description> |
| 4 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"> | |
| 3 | 7 <requirement type="package" version="4.1.0">gnu_awk</requirement> |
| 4 | 8 </expand> |
| 9 <version_command>awk --version | head -n 1</version_command> | |
| 6 | 10 <command> |
| 4 | 11 <![CDATA[ |
| 12 awk | |
| 6 | 13 -v OFS=" " |
| 4 | 14 --re-interval |
| 6 | 15 --sandbox '{ \$$column = gensub( /$find_pattern/, "$replace_pattern", "g", \$$column ) ; print \$0 ; }' |
| 4 | 16 "$infile" |
| 6 | 17 > "$outfile" |
| 4 | 18 ]]> |
| 3 | 19 </command> |
| 20 <inputs> | |
| 4 | 21 <param format="tabular" name="infile" type="data" label="File to process" /> |
| 22 <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" /> | |
| 3 | 23 |
|
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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 // ) " > |
| 3 | 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" help="Use simple text, or & (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." > |
| 3 | 32 <sanitizer> |
| 33 <valid initial="string.printable"> | |
| 34 <remove value="'"/> | |
| 35 </valid> | |
| 36 </sanitizer> | |
| 37 </param> | |
| 38 </inputs> | |
| 4 | 39 <outputs> |
| 6 | 40 <data name="outfile" format_source="infile" metadata_source="infile" /> |
| 4 | 41 </outputs> |
| 3 | 42 <tests> |
| 43 <test> | |
| 6 | 44 <param name="infile" value="replace_text_in_column1.txt" ftype="tabular" /> |
| 4 | 45 <param name="column" value="4" /> |
| 46 <param name="find_pattern" value=".+_(R.)" /> | |
| 6 | 47 <param name="replace_pattern" value="\\1" /> |
| 48 <output name="outfile" file="replace_text_in_column_results1.txt" /> | |
| 3 | 49 </test> |
| 50 </tests> | |
| 51 <help> | |
| 4 | 52 <![CDATA[ |
| 3 | 53 **What it does** |
| 54 | |
| 6 | 55 This tool performs find & replace operation on a specified column in a given file. |
| 3 | 56 |
| 57 .. class:: infomark | |
| 58 | |
| 59 The **pattern to find** uses the **extended regular** expression syntax (same as running 'awk --re-interval'). | |
| 60 | |
| 61 .. class:: infomark | |
| 62 | |
| 63 **TIP:** If you need more complex patterns, use the *awk* tool. | |
| 64 | |
| 65 ----- | |
| 66 | |
| 67 | |
| 68 **Examples of Find Patterns** | |
| 69 | |
| 70 - **HELLO** The word 'HELLO' (case sensitive). | |
| 71 - **AG.T** The letters A,G followed by any single character, followed by the letter T. | |
| 72 - **A{4,}** Four or more consecutive A's. | |
| 73 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character. | |
| 74 - **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. | |
| 75 | |
| 76 | |
| 77 **Examples of Replace Patterns** | |
| 78 | |
| 79 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found. | |
| 6 | 80 - **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 | 81 - **\\1** The text which matched the first parenthesis in the Find Pattern. |
| 82 | |
| 83 | |
| 84 ----- | |
| 85 | |
| 86 **Example 1** | |
| 87 | |
| 88 **Find Pattern:** HELLO | |
| 89 **Replace Pattern:** WORLD | |
| 90 | |
| 91 Every time the word HELLO is found, it will be replaced with the word WORLD. This operation affects only the selected column. | |
| 92 | |
| 93 ----- | |
| 94 | |
| 95 **Example 2** | |
| 96 | |
| 7 | 97 **Find Pattern:** ^(.{4}) |
| 6 | 98 **Replace Pattern:** &\\t |
| 3 | 99 |
| 100 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. This operation affects only the selected column. | |
| 101 | |
| 102 | |
| 103 ----- | |
| 104 | |
| 105 **Extened Regular Expression Syntax** | |
| 106 | |
| 7 | 107 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 | 108 |
| 109 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. | |
| 110 - **^** matches the beginning of a string(but not an internal line). | |
| 111 - **(** .. **)** groups a particular pattern. | |
| 112 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. | |
| 113 | |
| 114 - **{n}** The preceding item is matched exactly n times. | |
| 7 | 115 - **{n,}** The preceding item ismatched n or more times. |
| 116 - **{n,m}** The preceding item is matched at least n times but not more than m times. | |
| 3 | 117 |
| 118 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**. | |
| 119 - **.** Matches any single character except a newline. | |
| 120 - ***** The preceding item will be matched zero or more times. | |
| 121 - **?** The preceding item is optional and matched at most once. | |
| 122 - **+** The preceding item will be matched one or more times. | |
| 123 - **^** has two meaning: | |
| 7 | 124 - matches the beginning of a line or string. |
| 3 | 125 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. |
| 126 - **$** matches the end of a line or string. | |
| 7 | 127 - **\|** Separates alternate possibilities. |
| 3 | 128 |
| 129 | |
| 130 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. | |
| 131 | |
| 4 | 132 @REFERENCES@ |
| 133 ]]> | |
| 3 | 134 </help> |
| 135 </tool> |