text_processing: grep.xml annotate

annotate grep.xml @ 18:1e974b82380d draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7

author	bgruening
date	Tue, 27 Feb 2018 17:10:53 -0500
parents	7725ab6dab67
children	f22a309187a3

rev	line source
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	1 <tool id="tp_grep_tool" name="Search in textfiles" version="@BASE_VERSION@.1">
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	2 <description>(grep)</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>
12 062ed2bb4f2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f8896018f5b980a456c4ceaffe0ed457dc80b5a8 bgruening parents: 10 diff changeset	7 <requirement type="package" version="2.14">grep</requirement>
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	8 <requirement type="package" version="4.4">sed</requirement><!-- for ansi2html.sh -->
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	9 </requirements>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	10 <version_command>grep --version \| head -n 1</version_command>
2 fc862d5bccaf Uploaded bgruening parents: 1 diff changeset	11 <command>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	12 <![CDATA[
2 fc862d5bccaf Uploaded bgruening parents: 1 diff changeset	13 #if str($color) == "COLOR":
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	14 GREP_COLOR='1;34'
56e80527c482 Uploaded bgruening parents: 3 diff changeset	15 grep
56e80527c482 Uploaded bgruening parents: 3 diff changeset	16 --color=always
10 c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	17 $regex_type
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	18 -A $lines_after
56e80527c482 Uploaded bgruening parents: 3 diff changeset	19 -B $lines_before
56e80527c482 Uploaded bgruening parents: 3 diff changeset	20 $invert
56e80527c482 Uploaded bgruening parents: 3 diff changeset	21 $case_sensitive
56e80527c482 Uploaded bgruening parents: 3 diff changeset	22 -- "${url_paste}"
8 fa7f88da29d7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 369e40078146d00608d52205bb8cee66ae735b76-dirty bgruening parents: 7 diff changeset	23 '${infile}' \| $__tool_directory__/ansi2html.sh > "${output}"
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	24 #else:
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	25 grep
10 c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	26 $regex_type
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	27 -A $lines_after
56e80527c482 Uploaded bgruening parents: 3 diff changeset	28 -B $lines_before
56e80527c482 Uploaded bgruening parents: 3 diff changeset	29 $invert
56e80527c482 Uploaded bgruening parents: 3 diff changeset	30 $case_sensitive
56e80527c482 Uploaded bgruening parents: 3 diff changeset	31 -- "${url_paste}"
56e80527c482 Uploaded bgruening parents: 3 diff changeset	32 '${infile}' \| grep -v "^--$" > "${output}"
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	33 #end if
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	34 ]]>
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	35 </command>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	36 <inputs>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	37 <param name="infile" format="txt" type="data" label="Select lines from" />
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	38
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	39 <param name="invert" type="select" label="that">
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	40 <option value="">Match</option>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	41 <option value="-v">Don't Match</option>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	42 </param>
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	43
10 c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	44 <param name="regex_type" type="select" label="Type of regex">
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	45 <option value="-G">Basic</option>
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	46 <option value="-P" selected="true">Perl</option>
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	47 <option value="-E">Extended (egrep)</option>
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	48 </param>
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	49
10 c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	50 <param name="url_paste" type="text" label="Regular Expression" help="See below for more details">
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	51 <sanitizer>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	52 <valid initial="string.printable">
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	53 <remove value="'"/>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	54 </valid>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	55 </sanitizer>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	56 </param>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	57
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	58 <param name="case_sensitive" type="select" label="Match type" help="(-i)">
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	59 <option value="-i">case insensitive</option>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	60 <option value="">case sensitive</option>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	61 </param>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	62 <param name="lines_before" type="integer" value="0"
56e80527c482 Uploaded bgruening parents: 3 diff changeset	63 label="Show lines preceding the matched line" help="leave it at zero unless you know what you're doing. (-B)" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	64 <param name="lines_after" type="integer" value="0"
56e80527c482 Uploaded bgruening parents: 3 diff changeset	65 label="Show lines trailing the matched line" help="leave it at zero unless you know what you're doing. (-A)" />
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	66 <param name="color" type="select" label="Output">
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	67 <option value="NOCOLOR">text file (for further processing)</option>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	68 <option value="COLOR">Highlighted HTML (for easier viewing)</option>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	69 </param>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	70
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	71 </inputs>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	72 <outputs>
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	73 <data name="output" format_source="infile" metadata_source="infile">
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	74 <change_format>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	75 <when input="color" value="COLOR" format="html"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	76 </change_format>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	77 </data>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	78 </outputs>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	79 <tests>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	80 <test>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	81 <!-- grep a FASTA file for sequences with specific motif -->
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	82 <param name="infile" value="grep1.txt" />
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	83 <param name="case_sensitive" value="case sensitive" />
10 c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	84 <param name="regex_type" value="-P" />
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	85 <param name="invert" value="" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	86 <param name="url_paste" value="AA.{2}GT" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	87 <param name="lines_before" value="1" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	88 <param name="lines_after" value="0" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	89 <param name="color" value="NOCOLOR" />
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	90 <output name="output" file="grep_results1.txt" />
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	91 </test>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	92 <test>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	93 <!-- grep a FASTA file for sequences with specific motif -
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	94 show highlighed output -->
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	95 <param name="infile" value="grep1.txt" />
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	96 <param name="case_sensitive" value="case sensitive" />
10 c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	97 <param name="regex_type" value="-P" />
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	98 <param name="invert" value="" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	99 <param name="url_paste" value="AA.{2}GT" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	100 <param name="lines_before" value="0" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	101 <param name="lines_after" value="0" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	102 <param name="color" value="COLOR" />
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	103 <output name="output" file="grep_results2.html" />
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	104 </test>
10 c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	105 <test><!-- tests egrep -->
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	106 <param name="infile" value="egrep1.txt" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	107 <param name="case_sensitive" value="case sensitive" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	108 <param name="regex_type" value="-E" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	109 <param name="invert" value="" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	110 <param name="url_paste" value="[^ ]+" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	111 <param name="lines_before" value="0" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	112 <param name="lines_after" value="0" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	113 <param name="color" value="NOCOLOR" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	114 <output name="output" file="egrep_results1.txt" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	115 </test>
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	116 <test><!-- same regex as egrep test, but different outcome with basic regex -->
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	117 <param name="infile" value="egrep1.txt" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	118 <param name="case_sensitive" value="case sensitive" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	119 <param name="regex_type" value="-G" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	120 <param name="invert" value="" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	121 <param name="url_paste" value="[^ ]+" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	122 <param name="lines_before" value="0" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	123 <param name="lines_after" value="0" />
c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	124 <param name="color" value="NOCOLOR" />
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	125 <output name="output" file="egrep_results2.txt" />
10 c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 8 diff changeset	126 </test>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	127 </tests>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	128 <help>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	129 <![CDATA[
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	130 What it does
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	131
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	132 This tool runs the unix grep command on the selected data file.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	133
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	134 .. class:: infomark
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	135
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	136 TIP: This tool uses the perl regular expression syntax (same as running 'grep -P'). This is NOT the POSIX or POSIX-extended syntax (unlike the awk/sed tools).
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	137
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	138
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	139 Further reading
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	140
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	141 - Wikipedia's Regular Expression page (http://en.wikipedia.org/wiki/Regular_expression)
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	142 - Regular Expressions cheat-sheet (PDF) (http://www.addedbytes.com/cheat-sheets/download/regular-expressions-cheat-sheet-v2.pdf)
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	143 - Grep Tutorial (http://www.panix.com/~elflord/unix/grep.html)
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	144
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	145 -----
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	146
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	147 Grep Examples
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	148
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	149 - AGC.AAT would match lines with AGC followed by any character, followed by AAT (e.g. AGCQAAT, AGCPAAT, AGCwAAT)
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	150 - C{2,5}AGC would match lines with 2 to 5 consecutive Cs followed by AGC
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	151 - TTT.{4,10}AAA would match lines with 3 Ts, followed by 4 to 10 characters (any characeters), followed by 3 As.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	152 - ^chr([0-9A-Za-z])+ would match lines that begin with chromsomes, such as lines in a BED format file.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	153 - (ACGT){1,5} would match at least 1 "ACGT" and at most 5 "ACGT" consecutively.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	154 - hsa\|mmu would match lines containing "hsa" or "mmu" (or both).
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	155
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	156 -----
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	157
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	158 Regular Expression Syntax
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	159
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	160 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.
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	161
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	162 - *( ) { } [ ] . ? + \ ^ $ are all special characters. \\** can be used to "escape" a special character, allowing that special character to be searched for.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	163 - ^ matches the beginning of a string(but not an internal line).
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	164 - \\d matches a digit, same as [0-9].
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	165 - \\D matches a non-digit.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	166 - \\s matches a whitespace character.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	167 - \\S matches anything BUT a whitespace.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	168 - \\t matches a tab.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	169 - \\w matches an alphanumeric character ( A to Z, 0 to 9 and underscore )
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	170 - \\W matches anything but an alphanumeric character.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	171 - ( .. ) groups a particular pattern.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	172 - \\Z matches the end of a string(but not a internal line).
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	173 - { n or n, or n,m } specifies an expected number of repetitions of the preceding pattern.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	174
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	175 - {n} The preceding item is matched exactly n times.
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	176 - {n,} The preceding item ismatched n or more times.
d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	177 - {n,m} The preceding item is matched at least n times but not more than m times.
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	178
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	179 - [ ... ] 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.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	180 - . Matches any single character except a newline.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	181 - ***** The preceding item will be matched zero or more times.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	182 - ? The preceding item is optional and matched at most once.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	183 - + The preceding item will be matched one or more times.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	184 - ^ has two meaning:
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	185 - matches the beginning of a line or string.
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	186 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	187 - $ matches the end of a line or string.
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	188 - \\| Separates alternate possibilities.
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	189
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	190 @REFERENCES@
56e80527c482 Uploaded bgruening parents: 3 diff changeset	191 ]]>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	192 </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	193 <expand macro="citations" />
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	194 </tool>

Mercurial > repos > bgruening > text_processing

annotate grep.xml @ 18:1e974b82380d draft