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comparison grep.xml @ 0:ec66f9d90ef0 draft

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author bgruening
date Thu, 05 Sep 2013 04:58:21 -0400
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1 <tool id="unixtools_grep_tool" name="Search in textfiles" version="0.1.1">
2 <description>(grep)</description>
3 <requirements>
4 <requirement type="package" version="8.21">gnu_coreutils</requirement>
5 <requirement type="package" version="2.14">gnu_grep</requirement>
6 <requirement type="set_environment">UNIX_TOOLS_SCRIPT_PATH</requirement>
7 </requirements>
8 <command interpreter="sh">
9 #if $color = "COLOR":
10 GREP_COLOR='1;34' grep --color=always -P "$@" -- "${url_paste}" '${input}' | \$UNIX_TOOLS_SCRIPT_PATH/ansi2html.sh > "${output}"
11 #else:
12 grep -P "$@" -- "${url_paste}" '${input}' | grep -v "^--$" > "${output}"
13 #end if
14
15 ##grep_wrapper.sh '$input' '$output' '$url_paste' $color -A $lines_after -B $lines_before $invert $case_sensitive
16 </command>
17 <inputs>
18 <param format="txt" name="input" type="data" label="Select lines from" />
19
20 <param name="invert" type="select" label="that">
21 <option value="">Match</option>
22 <option value="-v">Don't Match</option>
23 </param>
24
25 <param name="url_paste" type="text" size="40" label="Regular Expression" help="See below for more details">
26 <sanitizer>
27 <valid initial="string.printable">
28 <remove value="&apos;"/>
29 </valid>
30 </sanitizer>
31 </param>
32
33 <param name="case_sensitive" type="select" label="Match type">
34 <option value="-i">case insensitive</option>
35 <option value="">case sensitive</option>
36 </param>
37
38 <param name="lines_before" type="integer" label="Show lines preceding the matched line (-B)" help="leave it at zero unless you know what you're doing" value="0" />
39 <param name="lines_after" type="integer" label="Show lines trailing the matched line (-A)" help="leave it at zero unless you know what you're doing" value="0" />
40
41 <param name="color" type="select" label="Output">
42 <option value="NOCOLOR">text file (for further processing)</option>
43 <option value="COLOR">Highlighted HTML (for easier viewing)</option>
44 </param>
45
46 </inputs>
47 <outputs>
48 <data format="input" name="output" metadata_source="input">
49 <change_format>
50 <when input="color" value="COLOR" format="html"
51 />
52 </change_format>
53 </data>
54 </outputs>
55 <tests>
56 <test>
57 <!-- grep a FASTA file for sequences with specific motif -->
58 <param name="input" value="unix_grep_input1.txt" />
59 <output name="output" file="unix_grep_output1.txt" />
60 <param name="case_sensitive" value="case sensitive" />
61 <param name="invert" value="" />
62 <param name="url_paste" value="AA.{2}GT" />
63 <param name="lines_before" value="1" />
64 <param name="lines_after" value="0" />
65 <param name="color" value="NOCOLOR" />
66 </test>
67 <test>
68 <!-- grep a FASTA file for sequences with specific motif -
69 show highlighed output -->
70 <param name="input" value="unix_grep_input1.txt" />
71 <output name="output" file="unix_grep_output2.html" />
72 <param name="case_sensitive" value="case sensitive" />
73 <param name="invert" value="" />
74 <param name="url_paste" value="AA.{2}GT" />
75 <param name="lines_before" value="0" />
76 <param name="lines_after" value="0" />
77 <param name="color" value="COLOR" />
78 </test>
79 </tests>
80 <help>
81
82 **What it does**
83
84 This tool runs the unix **grep** command on the selected data file.
85
86 .. class:: infomark
87
88 **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).
89
90
91 **Further reading**
92
93 - Wikipedia's Regular Expression page (http://en.wikipedia.org/wiki/Regular_expression)
94 - Regular Expressions cheat-sheet (PDF) (http://www.addedbytes.com/cheat-sheets/download/regular-expressions-cheat-sheet-v2.pdf)
95 - Grep Tutorial (http://www.panix.com/~elflord/unix/grep.html)
96
97 -----
98
99 **Grep Examples**
100
101 - **AGC.AAT** would match lines with AGC followed by any character, followed by AAT (e.g. **AGCQAAT**, **AGCPAAT**, **AGCwAAT**)
102 - **C{2,5}AGC** would match lines with 2 to 5 consecutive Cs followed by AGC
103 - **TTT.{4,10}AAA** would match lines with 3 Ts, followed by 4 to 10 characters (any characeters), followed by 3 As.
104 - **^chr([0-9A-Za-z])+** would match lines that begin with chromsomes, such as lines in a BED format file.
105 - **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively.
106 - **hsa|mmu** would match lines containing "hsa" or "mmu" (or both).
107
108 -----
109
110 **Regular Expression Syntax**
111
112 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.
113
114 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
115 - **^** matches the beginning of a string(but not an internal line).
116 - **\\d** matches a digit, same as [0-9].
117 - **\\D** matches a non-digit.
118 - **\\s** matches a whitespace character.
119 - **\\S** matches anything BUT a whitespace.
120 - **\\t** matches a tab.
121 - **\\w** matches an alphanumeric character ( A to Z, 0 to 9 and underscore )
122 - **\\W** matches anything but an alphanumeric character.
123 - **(** .. **)** groups a particular pattern.
124 - **\\Z** matches the end of a string(but not a internal line).
125 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
126
127 - **{n}** The preceding item is matched exactly n times.
128 - **{n,}** The preceding item ismatched n or more times.
129 - **{n,m}** The preceding item is matched at least n times but not more than m times.
130
131 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
132 - **.** Matches any single character except a newline.
133 - ***** The preceding item will be matched zero or more times.
134 - **?** The preceding item is optional and matched at most once.
135 - **+** The preceding item will be matched one or more times.
136 - **^** has two meaning:
137 - matches the beginning of a line or string.
138 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
139 - **$** matches the end of a line or string.
140 - **\|** Separates alternate possibilities.
141
142
143 </help>
144 </tool>