Mercurial > repos > bgruening > text_processing
annotate replace_text_in_column.xml @ 16:61b3b01662fd draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 5d3a6a822897569f22f288589543562f54482418
| author | bgruening |
|---|---|
| date | Fri, 01 Dec 2017 13:46:51 -0500 |
| parents | 7725ab6dab67 |
| children | 1e974b82380d |
| rev | line source |
|---|---|
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7725ab6dab67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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1 <tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.1"> |
| 3 | 2 <description>in a specific column</description> |
| 4 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
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3c685c4106b3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
bgruening
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6 <requirements> |
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062ed2bb4f2e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f8896018f5b980a456c4ceaffe0ed457dc80b5a8
bgruening
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7 <requirement type="package" version="4.1.3">gawk</requirement> |
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3c685c4106b3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
bgruening
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8 </requirements> |
| 4 | 9 <version_command>awk --version | head -n 1</version_command> |
| 6 | 10 <command> |
| 4 | 11 <![CDATA[ |
| 12 awk | |
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7725ab6dab67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
13
diff
changeset
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13 -v OFS="\t" |
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7725ab6dab67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
13
diff
changeset
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14 -v FS="\t" |
| 4 | 15 --re-interval |
| 6 | 16 --sandbox '{ \$$column = gensub( /$find_pattern/, "$replace_pattern", "g", \$$column ) ; print \$0 ; }' |
| 4 | 17 "$infile" |
| 6 | 18 > "$outfile" |
| 4 | 19 ]]> |
| 3 | 20 </command> |
| 21 <inputs> | |
| 4 | 22 <param format="tabular" name="infile" type="data" label="File to process" /> |
| 23 <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" /> | |
| 3 | 24 |
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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
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25 <param name="find_pattern" type="text" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > |
| 3 | 26 <sanitizer> |
| 27 <valid initial="string.printable"> | |
| 28 <remove value="'"/> | |
| 29 </valid> | |
| 30 </sanitizer> | |
| 31 </param> | |
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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
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32 <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 | 33 <sanitizer> |
| 34 <valid initial="string.printable"> | |
| 35 <remove value="'"/> | |
| 36 </valid> | |
| 37 </sanitizer> | |
| 38 </param> | |
| 39 </inputs> | |
| 4 | 40 <outputs> |
| 6 | 41 <data name="outfile" format_source="infile" metadata_source="infile" /> |
| 4 | 42 </outputs> |
| 3 | 43 <tests> |
| 44 <test> | |
| 6 | 45 <param name="infile" value="replace_text_in_column1.txt" ftype="tabular" /> |
| 4 | 46 <param name="column" value="4" /> |
| 47 <param name="find_pattern" value=".+_(R.)" /> | |
| 6 | 48 <param name="replace_pattern" value="\\1" /> |
| 49 <output name="outfile" file="replace_text_in_column_results1.txt" /> | |
| 3 | 50 </test> |
| 51 </tests> | |
| 52 <help> | |
| 4 | 53 <![CDATA[ |
| 3 | 54 **What it does** |
| 55 | |
| 6 | 56 This tool performs find & replace operation on a specified column in a given file. |
| 3 | 57 |
| 58 .. class:: infomark | |
| 59 | |
| 60 The **pattern to find** uses the **extended regular** expression syntax (same as running 'awk --re-interval'). | |
| 61 | |
| 62 .. class:: infomark | |
| 63 | |
| 64 **TIP:** If you need more complex patterns, use the *awk* tool. | |
| 65 | |
| 66 ----- | |
| 67 | |
| 68 | |
| 69 **Examples of Find Patterns** | |
| 70 | |
| 71 - **HELLO** The word 'HELLO' (case sensitive). | |
| 72 - **AG.T** The letters A,G followed by any single character, followed by the letter T. | |
| 73 - **A{4,}** Four or more consecutive A's. | |
| 74 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character. | |
| 75 - **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. | |
| 76 | |
| 77 | |
| 78 **Examples of Replace Patterns** | |
| 79 | |
| 80 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found. | |
| 6 | 81 - **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 | 82 - **\\1** The text which matched the first parenthesis in the Find Pattern. |
| 83 | |
| 84 | |
| 85 ----- | |
| 86 | |
| 87 **Example 1** | |
| 88 | |
| 89 **Find Pattern:** HELLO | |
| 90 **Replace Pattern:** WORLD | |
| 91 | |
| 92 Every time the word HELLO is found, it will be replaced with the word WORLD. This operation affects only the selected column. | |
| 93 | |
| 94 ----- | |
| 95 | |
| 96 **Example 2** | |
| 97 | |
| 7 | 98 **Find Pattern:** ^(.{4}) |
| 6 | 99 **Replace Pattern:** &\\t |
| 3 | 100 |
| 101 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. | |
| 102 | |
| 103 | |
| 104 ----- | |
| 105 | |
| 106 **Extened Regular Expression Syntax** | |
| 107 | |
| 7 | 108 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 | 109 |
| 110 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. | |
| 111 - **^** matches the beginning of a string(but not an internal line). | |
| 112 - **(** .. **)** groups a particular pattern. | |
| 113 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. | |
| 114 | |
| 115 - **{n}** The preceding item is matched exactly n times. | |
| 7 | 116 - **{n,}** The preceding item ismatched n or more times. |
| 117 - **{n,m}** The preceding item is matched at least n times but not more than m times. | |
| 3 | 118 |
| 119 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**. | |
| 120 - **.** Matches any single character except a newline. | |
| 121 - ***** The preceding item will be matched zero or more times. | |
| 122 - **?** The preceding item is optional and matched at most once. | |
| 123 - **+** The preceding item will be matched one or more times. | |
| 124 - **^** has two meaning: | |
| 7 | 125 - matches the beginning of a line or string. |
| 3 | 126 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. |
| 127 - **$** matches the end of a line or string. | |
| 7 | 128 - **\|** Separates alternate possibilities. |
| 3 | 129 |
| 130 | |
| 131 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. | |
| 132 | |
| 4 | 133 @REFERENCES@ |
| 134 ]]> | |
| 3 | 135 </help> |
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7725ab6dab67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
13
diff
changeset
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136 <expand macro="citations" /> |
| 3 | 137 </tool> |