Mercurial > repos > bgruening > text_processing
diff replace_text_in_column.xml @ 0:5314e5d6f040 draft
Imported from capsule None
author | bgruening |
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date | Thu, 29 Jan 2015 07:53:17 -0500 |
parents | |
children | 37e1eb05b1b4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/replace_text_in_column.xml Thu Jan 29 07:53:17 2015 -0500 @@ -0,0 +1,135 @@ +<tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.0"> + <description>in a specific column</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="4.1.0">gnu_awk</requirement> + </expand> + <version_command>awk --version | head -n 1</version_command> + <command> +<![CDATA[ + awk + -v OFS=" " + --re-interval + --sandbox '{ \$$column = gensub( /$find_pattern/, "$replace_pattern", "g", \$$column ) ; print \$0 ; }' + "$infile" + > "$outfile" +]]> + </command> + <inputs> + <param format="tabular" name="infile" type="data" label="File to process" /> + <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" /> + + <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + <param name="replace_pattern" 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." > + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + </inputs> + <outputs> + <data name="outfile" format_source="infile" metadata_source="infile" /> + </outputs> + <tests> + <test> + <param name="infile" value="replace_text_in_column1.txt" ftype="tabular" /> + <param name="column" value="4" /> + <param name="find_pattern" value=".+_(R.)" /> + <param name="replace_pattern" value="\\1" /> + <output name="outfile" file="replace_text_in_column_results1.txt" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +This tool performs find & replace operation on a specified column in a given file. + +.. class:: infomark + +The **pattern to find** uses the **extended regular** expression syntax (same as running 'awk --re-interval'). + +.. class:: infomark + +**TIP:** If you need more complex patterns, use the *awk* tool. + +----- + + +**Examples of Find Patterns** + +- **HELLO** The word 'HELLO' (case sensitive). +- **AG.T** The letters A,G followed by any single character, followed by the letter T. +- **A{4,}** Four or more consecutive A's. +- **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character. +- **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. + + +**Examples of Replace Patterns** + +- **WORLD** The word 'WORLD' will be placed whereever the find pattern was found. +- **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. +- **\\1** The text which matched the first parenthesis in the Find Pattern. + + +----- + +**Example 1** + +**Find Pattern:** HELLO +**Replace Pattern:** WORLD + +Every time the word HELLO is found, it will be replaced with the word WORLD. This operation affects only the selected column. + +----- + +**Example 2** + +**Find Pattern:** ^(.{4}) +**Replace Pattern:** &\\t + +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. + + +----- + +**Extened Regular Expression Syntax** + +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. + +- **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. +- **^** matches the beginning of a string(but not an internal line). +- **(** .. **)** groups a particular pattern. +- **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. + + - **{n}** The preceding item is matched exactly n times. + - **{n,}** The preceding item ismatched n or more times. + - **{n,m}** The preceding item is matched at least n times but not more than m times. + +- **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**. +- **.** Matches any single character except a newline. +- ***** The preceding item will be matched zero or more times. +- **?** The preceding item is optional and matched at most once. +- **+** The preceding item will be matched one or more times. +- **^** has two meaning: + - matches the beginning of a line or string. + - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. +- **$** matches the end of a line or string. +- **\|** Separates alternate possibilities. + + +**Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. + +@REFERENCES@ +]]> + </help> +</tool>