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