text_processing: grep.xml annotate

annotate grep.xml @ 27:08cdbfffce67 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b

author	bgruening
date	Fri, 07 Mar 2025 20:43:41 +0000
parents	f22a309187a3
children

rev	line source
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	1 <tool id="tp_grep_tool" name="Search in textfiles" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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>
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	6 <expand macro="creator"/>
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	7 <requirements>
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	8 <requirement type="package" version="3.11">grep</requirement>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	9 <requirement type="package" version="4.8">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	10 </requirements>
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	11 <stdio>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	12 <exit_code range="2:" level="fatal" description="grep failed" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	13 </stdio>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	14 <version_command>grep --version \| head -n 1</version_command>
2 fc862d5bccaf Uploaded bgruening parents: 1 diff changeset	15 <command>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	16 <![CDATA[
2 fc862d5bccaf Uploaded bgruening parents: 1 diff changeset	17 #if str($color) == "COLOR":
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	18 GREP_COLOR='1;34'
56e80527c482 Uploaded bgruening parents: 3 diff changeset	19 grep
56e80527c482 Uploaded bgruening parents: 3 diff changeset	20 --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	21 $regex_type
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	22 -A $lines_after
56e80527c482 Uploaded bgruening parents: 3 diff changeset	23 -B $lines_before
56e80527c482 Uploaded bgruening parents: 3 diff changeset	24 $invert
56e80527c482 Uploaded bgruening parents: 3 diff changeset	25 $case_sensitive
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	26 -- '${url_paste}'
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	27 '${infile}' \| '$__tool_directory__/ansi2html.sh' > '${output}'
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	28 #else:
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	29 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	30 $regex_type
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	31 -A $lines_after
56e80527c482 Uploaded bgruening parents: 3 diff changeset	32 -B $lines_before
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	33 --no-group-separator
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	34 $invert
56e80527c482 Uploaded bgruening parents: 3 diff changeset	35 $case_sensitive
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	36 -- '${url_paste}'
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	37 '${infile}' > '${output}'
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	38 #end if
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	39 ]]>
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	40 </command>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	41 <inputs>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	42 <param name="infile" format="txt" type="data" label="Select lines from" />
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	43
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	44 <param name="invert" type="select" label="that">
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	45 <option value="">Match</option>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	46 <option value="-v">Don't Match</option>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	47 </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	48
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	49 <param name="regex_type" type="select" label="Type of regex">
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	50 <option value="-G">Basic (-G)</option>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	51 <option value="-P" selected="true">Perl (-P)</option>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	52 <option value="-E">Extended (egrep -E)</option>
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	53 </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	54
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	55 <param name="url_paste" type="text" label="Regular Expression" help="See below for more details">
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	56 <sanitizer>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	57 <valid initial="string.printable">
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	58 <remove value="'"/>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	59 </valid>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	60 </sanitizer>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	61 </param>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	62
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	63 <param name="case_sensitive" type="select" label="Match type" help="(-i)">
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	64 <option value="-i">case insensitive</option>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	65 <option value="">case sensitive</option>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	66 </param>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	67 <param name="lines_before" type="integer" value="0"
56e80527c482 Uploaded bgruening parents: 3 diff changeset	68 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	69 <param name="lines_after" type="integer" value="0"
56e80527c482 Uploaded bgruening parents: 3 diff changeset	70 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	71 <param name="color" type="select" label="Output">
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	72 <option value="NOCOLOR">text file (for further processing)</option>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	73 <option value="COLOR">Highlighted HTML (for easier viewing)</option>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	74 </param>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	75
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	76 </inputs>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	77 <outputs>
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	78 <data name="output" format_source="infile" metadata_source="infile">
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	79 <change_format>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	80 <when input="color" value="COLOR" format="html"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	81 </change_format>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	82 </data>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	83 </outputs>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	84 <tests>
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	85 <!-- grep a FASTA file for sequences with specific motif -->
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	86 <test>
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	87 <param name="infile" value="grep1.txt" />
27 08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	88 <param name="case_sensitive" value="-i" />
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	89 <param name="regex_type" value="-P" />
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	90 <param name="invert" value="" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	91 <param name="url_paste" value="AA.{2}GT" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	92 <param name="lines_before" value="1" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	93 <param name="lines_after" value="0" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	94 <param name="color" value="NOCOLOR" />
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	95 <output name="output" file="grep_results1.txt" />
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	96 </test>
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	97 <!-- grep a FASTA file for sequences with specific motif -
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	98 show highlighed output -->
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	99 <test>
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	100 <param name="infile" value="grep1.txt" />
27 08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	101 <param name="case_sensitive" value="-i" />
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	102 <param name="regex_type" value="-P" />
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	103 <param name="invert" value="" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	104 <param name="url_paste" value="AA.{2}GT" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	105 <param name="lines_before" value="0" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	106 <param name="lines_after" value="0" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	107 <param name="color" value="COLOR" />
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	108 <output name="output" file="grep_results2.html" />
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	109 </test>
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	110 <!-- tests egrep -->
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	111 <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	112 <param name="infile" value="egrep1.txt" />
27 08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	113 <param name="case_sensitive" value="-i" />
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	114 <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	115 <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	116 <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	117 <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	118 <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	119 <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	120 <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	121 </test>
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	122 <!-- tests basic regex; + must be backslashed to match -->
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	123 <test>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	124 <param name="infile" value="egrep1.txt" />
27 08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	125 <param name="case_sensitive" value="-i" />
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	126 <param name="regex_type" value="-G" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	127 <param name="invert" value="" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	128 <param name="url_paste" value="[^ ]\+" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	129 <param name="lines_before" value="0" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	130 <param name="lines_after" value="0" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	131 <param name="color" value="NOCOLOR" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	132 <output name="output" file="egrep_results1.txt" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	133 </test>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	134 <!-- tests regex;matching nothing -->
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	135 <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	136 <param name="infile" value="egrep1.txt" />
27 08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	137 <param name="case_sensitive" value="-i" />
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	138 <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	139 <param name="invert" value="" />
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	140 <param name="url_paste" value="not existent pattern" />
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	141 <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	142 <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	143 <param name="color" value="NOCOLOR" />
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	144 <output name="output">
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	145 <assert_contents>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	146 <has_size value="0"/>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	147 </assert_contents>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	148 </output>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	149 </test>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	150 <!-- tests invalid regex; i.e. that we still get exit code 2 -->
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	151 <test expect_failure="true" expect_exit_code="2">
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	152 <param name="infile" value="egrep1.txt" />
27 08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	153 <param name="case_sensitive" value="-i" />
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	154 <param name="regex_type" value="-G" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	155 <param name="invert" value="" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	156 <param name="url_paste" value="\(" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	157 <param name="lines_before" value="0" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	158 <param name="lines_after" value="0" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 18 diff changeset	159 <param name="color" value="NOCOLOR" />
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	160 </test>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	161 </tests>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	162 <help>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	163 <![CDATA[
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	164 What it does
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	165
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	166 This tool runs the unix grep command on the selected data file.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	167
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	168 .. class:: infomark
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	169
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	170 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	171
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	172
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	173 Further reading
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	174
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	175 - Wikipedia's Regular Expression page (http://en.wikipedia.org/wiki/Regular_expression)
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	176 - 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	177 - Grep Tutorial (http://www.panix.com/~elflord/unix/grep.html)
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	178
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	179 -----
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	180
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	181 Grep Examples
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	182
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	183 - 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	184 - C{2,5}AGC would match lines with 2 to 5 consecutive Cs followed by AGC
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	185 - 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	186 - ^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	187 - (ACGT){1,5} would match at least 1 "ACGT" and at most 5 "ACGT" consecutively.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	188 - hsa\|mmu would match lines containing "hsa" or "mmu" (or both).
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	189
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	190 -----
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	191
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	192 Regular Expression Syntax
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	193
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	194 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	195
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	196 - *( ) { } [ ] . ? + \ ^ $ 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	197 - ^ matches the beginning of a string(but not an internal line).
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	198 - \\d matches a digit, same as [0-9].
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	199 - \\D matches a non-digit.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	200 - \\s matches a whitespace character.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	201 - \\S matches anything BUT a whitespace.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	202 - \\t matches a tab.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	203 - \\w matches an alphanumeric character ( A to Z, 0 to 9 and underscore )
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	204 - \\W matches anything but an alphanumeric character.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	205 - ( .. ) groups a particular pattern.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	206 - \\Z matches the end of a string(but not a internal line).
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	207 - { n or n, or n,m } specifies an expected number of repetitions of the preceding pattern.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	208
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	209 - {n} The preceding item is matched exactly n times.
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	210 - {n,} The preceding item ismatched n or more times.
d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	211 - {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	212
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	213 - [ ... ] 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	214 - . Matches any single character except a newline.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	215 - ***** The preceding item will be matched zero or more times.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	216 - ? The preceding item is optional and matched at most once.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	217 - + The preceding item will be matched one or more times.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	218 - ^ has two meaning:
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	219 - matches the beginning of a line or string.
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	220 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	221 - $ matches the end of a line or string.
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	222 - \\| Separates alternate possibilities.
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	223
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	224 ]]>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	225 </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	226 <expand macro="citations" />
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	227 </tool>

Mercurial > repos > bgruening > text_processing

annotate grep.xml @ 27:08cdbfffce67 draft