text_processing: replace_text_in

annotate replace_text_in_column.xml @ 21:0e3b611245f7 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 9c4d4fe09cbbd818532d793d01d1cb16edbd496b-dirty"

author	bgruening
date	Sun, 15 Mar 2020 22:58:18 +0000
parents	bed2226b90f7
children	f22a309187a3

rev	line source
19 bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	1 <tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.3">
3 7068d1548234 Uploaded bgruening parents: diff changeset	2 <description>in a specific column</description>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	3 <macros>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	4 <import>macros.xml</import>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	5 </macros>
13 3c685c4106b3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52 bgruening parents: 12 diff changeset	6 <requirements>
18 1e974b82380d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7 bgruening parents: 14 diff changeset	7 <requirement type="package" version="4.2.0">gawk</requirement>
13 3c685c4106b3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52 bgruening parents: 12 diff changeset	8 </requirements>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	9 <version_command>awk --version \| head -n 1</version_command>
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	10 <command>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	11 <![CDATA[
56e80527c482 Uploaded bgruening parents: 3 diff changeset	12 awk
14 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	13 -v OFS="\t"
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	14 -v FS="\t"
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	15 --re-interval
19 bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	16 --sandbox
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	17 '{
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	18 #for $replacement in $replacements:
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	19 \$$replacement.column = gensub( /$replacement.find_pattern/, "$replacement.replace_pattern", "g", \$$replacement.column ) ;
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	20 #end for
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	21 print \$0 ; }'
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	22 "$infile"
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	23 > "$outfile"
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	24 ]]>
3 7068d1548234 Uploaded bgruening parents: diff changeset	25 </command>
7068d1548234 Uploaded bgruening parents: diff changeset	26 <inputs>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	27 <param format="tabular" name="infile" type="data" label="File to process" />
19 bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	28 <repeat name="replacements" title="Replacement" min="1">
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	29 <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" />
3 7068d1548234 Uploaded bgruening parents: diff changeset	30
19 bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	31 <param name="find_pattern" type="text" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	32 <sanitizer>
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	33 <valid initial="string.printable">
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	34 <remove value="'"/>
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	35 </valid>
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	36 </sanitizer>
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	37 </param>
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	38 <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." >
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	39 <sanitizer>
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	40 <valid initial="string.printable">
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	41 <remove value="'"/>
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	42 </valid>
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	43 </sanitizer>
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	44 </param>
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	45 </repeat>
3 7068d1548234 Uploaded bgruening parents: diff changeset	46 </inputs>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	47 <outputs>
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	48 <data name="outfile" format_source="infile" metadata_source="infile" />
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	49 </outputs>
3 7068d1548234 Uploaded bgruening parents: diff changeset	50 <tests>
19 bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	51 <test>
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	52 <param name="infile" value="replace_text_in_column1.txt" ftype="tabular" />
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	53 <param name="column" value="4" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	54 <param name="find_pattern" value=".+_(R.)" />
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	55 <param name="replace_pattern" value="\\1" />
8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	56 <output name="outfile" file="replace_text_in_column_results1.txt" />
3 7068d1548234 Uploaded bgruening parents: diff changeset	57 </test>
19 bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	58 <test>
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	59 <param name="infile" value="replace_text_in_column1.txt" ftype="tabular" />
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	60 <repeat name="replacements">
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	61 <param name="column" value="1" />
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	62 <param name="find_pattern" value="[a-z]{2}([a-z])" />
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	63 <param name="replace_pattern" value="\\1" />
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	64 </repeat>
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	65 <repeat name="replacements">
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	66 <param name="column" value="4" />
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	67 <param name="find_pattern" value=".+_(R.)" />
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	68 <param name="replace_pattern" value="\\1" />
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	69 </repeat>
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	70 <output name="outfile" file="replace_text_in_column_results2.txt" />
bed2226b90f7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 29899be24c03f631ef3be107fd60e9f898806321 bgruening parents: 18 diff changeset	71 </test>
3 7068d1548234 Uploaded bgruening parents: diff changeset	72 </tests>
7068d1548234 Uploaded bgruening parents: diff changeset	73 <help>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	74 <![CDATA[
3 7068d1548234 Uploaded bgruening parents: diff changeset	75 What it does
7068d1548234 Uploaded bgruening parents: diff changeset	76
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	77 This tool performs find & replace operation on a specified column in a given file.
3 7068d1548234 Uploaded bgruening parents: diff changeset	78
7068d1548234 Uploaded bgruening parents: diff changeset	79 .. class:: infomark
7068d1548234 Uploaded bgruening parents: diff changeset	80
7068d1548234 Uploaded bgruening parents: diff changeset	81 The pattern to find uses the extended regular expression syntax (same as running 'awk --re-interval').
7068d1548234 Uploaded bgruening parents: diff changeset	82
7068d1548234 Uploaded bgruening parents: diff changeset	83 .. class:: infomark
7068d1548234 Uploaded bgruening parents: diff changeset	84
7068d1548234 Uploaded bgruening parents: diff changeset	85 TIP: If you need more complex patterns, use the awk tool.
7068d1548234 Uploaded bgruening parents: diff changeset	86
7068d1548234 Uploaded bgruening parents: diff changeset	87 -----
7068d1548234 Uploaded bgruening parents: diff changeset	88
7068d1548234 Uploaded bgruening parents: diff changeset	89
7068d1548234 Uploaded bgruening parents: diff changeset	90 Examples of Find Patterns
7068d1548234 Uploaded bgruening parents: diff changeset	91
7068d1548234 Uploaded bgruening parents: diff changeset	92 - HELLO The word 'HELLO' (case sensitive).
7068d1548234 Uploaded bgruening parents: diff changeset	93 - AG.T The letters A,G followed by any single character, followed by the letter T.
7068d1548234 Uploaded bgruening parents: diff changeset	94 - A{4,} Four or more consecutive A's.
7068d1548234 Uploaded bgruening parents: diff changeset	95 - chr2[012]\\t The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
7068d1548234 Uploaded bgruening parents: diff changeset	96 - 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.
7068d1548234 Uploaded bgruening parents: diff changeset	97
7068d1548234 Uploaded bgruening parents: diff changeset	98
7068d1548234 Uploaded bgruening parents: diff changeset	99 Examples of Replace Patterns
7068d1548234 Uploaded bgruening parents: diff changeset	100
7068d1548234 Uploaded bgruening parents: diff changeset	101 - WORLD The word 'WORLD' will be placed whereever the find pattern was found.
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	102 - 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 7068d1548234 Uploaded bgruening parents: diff changeset	103 - \\1 The text which matched the first parenthesis in the Find Pattern.
7068d1548234 Uploaded bgruening parents: diff changeset	104
7068d1548234 Uploaded bgruening parents: diff changeset	105
7068d1548234 Uploaded bgruening parents: diff changeset	106 -----
7068d1548234 Uploaded bgruening parents: diff changeset	107
7068d1548234 Uploaded bgruening parents: diff changeset	108 Example 1
7068d1548234 Uploaded bgruening parents: diff changeset	109
7068d1548234 Uploaded bgruening parents: diff changeset	110 Find Pattern: HELLO
7068d1548234 Uploaded bgruening parents: diff changeset	111 Replace Pattern: WORLD
7068d1548234 Uploaded bgruening parents: diff changeset	112
7068d1548234 Uploaded bgruening parents: diff changeset	113 Every time the word HELLO is found, it will be replaced with the word WORLD. This operation affects only the selected column.
7068d1548234 Uploaded bgruening parents: diff changeset	114
7068d1548234 Uploaded bgruening parents: diff changeset	115 -----
7068d1548234 Uploaded bgruening parents: diff changeset	116
7068d1548234 Uploaded bgruening parents: diff changeset	117 Example 2
7068d1548234 Uploaded bgruening parents: diff changeset	118
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	119 Find Pattern: ^(.{4})
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	120 Replace Pattern: &\\t
3 7068d1548234 Uploaded bgruening parents: diff changeset	121
7068d1548234 Uploaded bgruening parents: diff changeset	122 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.
7068d1548234 Uploaded bgruening parents: diff changeset	123
7068d1548234 Uploaded bgruening parents: diff changeset	124
7068d1548234 Uploaded bgruening parents: diff changeset	125 -----
7068d1548234 Uploaded bgruening parents: diff changeset	126
7068d1548234 Uploaded bgruening parents: diff changeset	127 Extened Regular Expression Syntax
7068d1548234 Uploaded bgruening parents: diff changeset	128
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	129 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 7068d1548234 Uploaded bgruening parents: diff changeset	130
7068d1548234 Uploaded bgruening parents: diff changeset	131 - *( ) { } [ ] . ? + \ ^ $ are all special characters. \\** can be used to "escape" a special character, allowing that special character to be searched for.
7068d1548234 Uploaded bgruening parents: diff changeset	132 - ^ matches the beginning of a string(but not an internal line).
7068d1548234 Uploaded bgruening parents: diff changeset	133 - ( .. ) groups a particular pattern.
7068d1548234 Uploaded bgruening parents: diff changeset	134 - { n or n, or n,m } specifies an expected number of repetitions of the preceding pattern.
7068d1548234 Uploaded bgruening parents: diff changeset	135
7068d1548234 Uploaded bgruening parents: diff changeset	136 - {n} The preceding item is matched exactly n times.
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	137 - {n,} The preceding item ismatched n or more times.
d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	138 - {n,m} The preceding item is matched at least n times but not more than m times.
3 7068d1548234 Uploaded bgruening parents: diff changeset	139
7068d1548234 Uploaded bgruening parents: diff changeset	140 - [ ... ] 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.
7068d1548234 Uploaded bgruening parents: diff changeset	141 - . Matches any single character except a newline.
7068d1548234 Uploaded bgruening parents: diff changeset	142 - ***** The preceding item will be matched zero or more times.
7068d1548234 Uploaded bgruening parents: diff changeset	143 - ? The preceding item is optional and matched at most once.
7068d1548234 Uploaded bgruening parents: diff changeset	144 - + The preceding item will be matched one or more times.
7068d1548234 Uploaded bgruening parents: diff changeset	145 - ^ has two meaning:
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	146 - matches the beginning of a line or string.
3 7068d1548234 Uploaded bgruening parents: diff changeset	147 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
7068d1548234 Uploaded bgruening parents: diff changeset	148 - $ matches the end of a line or string.
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	149 - \\| Separates alternate possibilities.
3 7068d1548234 Uploaded bgruening parents: diff changeset	150
7068d1548234 Uploaded bgruening parents: diff changeset	151
7068d1548234 Uploaded bgruening parents: diff changeset	152 Note: AWK uses extended regular expression syntax, not Perl syntax. \\d, \\w, \\s etc. are not supported.
7068d1548234 Uploaded bgruening parents: diff changeset	153
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	154 @REFERENCES@
56e80527c482 Uploaded bgruening parents: 3 diff changeset	155 ]]>
3 7068d1548234 Uploaded bgruening parents: diff changeset	156 </help>
14 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	157 <expand macro="citations" />
3 7068d1548234 Uploaded bgruening parents: diff changeset	158 </tool>

Mercurial > repos > bgruening > text_processing

annotate replace_text_in_column.xml @ 21:0e3b611245f7 draft