|
4
|
1 <tool id="tp_awk_tool" name="Text reformatting" version="@BASE_VERSION@.0">
|
|
2
|
2 <description>with awk</description>
|
|
4
|
3 <macros>
|
|
|
4 <import>macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <expand macro="requirements">
|
|
0
|
7 <requirement type="package" version="4.1.0">gnu_awk</requirement>
|
|
4
|
8 </expand>
|
|
|
9 <version_command>awk --version | head -n 1</version_command>
|
|
0
|
10 <command>
|
|
4
|
11 <![CDATA[
|
|
|
12 awk
|
|
|
13 --sandbox
|
|
6
|
14 -v FS=' '
|
|
|
15 -v OFS=' '
|
|
4
|
16 --re-interval
|
|
6
|
17 -f "$awk_script"
|
|
|
18 "$infile"
|
|
|
19 > "$outfile"
|
|
4
|
20 ]]>
|
|
0
|
21 </command>
|
|
|
22 <inputs>
|
|
6
|
23 <param name="infile" format="txt" type="data" label="File to process" />
|
|
|
24 <param name="code" type="text" area="true" size="5x35" label="AWK Program" help="">
|
|
0
|
25 <sanitizer>
|
|
|
26 <valid initial="string.printable">
|
|
|
27 <remove value="'"/>
|
|
|
28 </valid>
|
|
|
29 </sanitizer>
|
|
|
30 </param>
|
|
4
|
31 </inputs>
|
|
|
32 <configfiles>
|
|
6
|
33 <configfile name="awk_script">$code</configfile>
|
|
4
|
34 </configfiles>
|
|
|
35 <outputs>
|
|
6
|
36 <data name="outfile" format_source="infile" metadata_source="infile"/>
|
|
4
|
37 </outputs>
|
|
|
38 <tests>
|
|
6
|
39 <test>
|
|
|
40 <param name="infile" value="awk1.txt" />
|
|
|
41 <!-- commas are not allowed in a value field. Values with comma will be splitted -->
|
|
|
42 <param name="code" value='$2>0.5 { print $2*9"\t"$1 }' />
|
|
|
43 <output name="outfile" file="awk_results1.txt" />
|
|
|
44 </test>
|
|
4
|
45 </tests>
|
|
|
46 <help>
|
|
|
47 <![CDATA[
|
|
0
|
48 **What it does**
|
|
|
49
|
|
|
50 This tool runs the unix **awk** command on the selected data file.
|
|
|
51
|
|
|
52 .. class:: infomark
|
|
|
53
|
|
7
|
54 **TIP:**
|
|
1
|
55
|
|
7
|
56 This tool uses the **extended regular** expression syntax (not the perl syntax).
|
|
1
|
57 **\\d**, **\\w**, **\\s** etc. are **not** supported.
|
|
0
|
58
|
|
|
59
|
|
|
60 **Further reading**
|
|
|
61
|
|
|
62 - Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1.html)
|
|
|
63 - Long AWK tutorial (http://www.grymoire.com/Unix/Awk.html)
|
|
|
64 - Learn AWK in 1 hour (http://www.selectorweb.com/awk.html)
|
|
|
65 - awk cheat-sheet (http://cbi.med.harvard.edu/people/peshkin/sb302/awk_cheatsheets.pdf)
|
|
|
66 - Collection of useful awk one-liners (http://student.northpark.edu/pemente/awk/awk1line.txt)
|
|
|
67
|
|
|
68 -----
|
|
|
69
|
|
|
70 **AWK programs**
|
|
|
71
|
|
|
72 Most AWK programs consist of **patterns** (i.e. rules that match lines of text) and **actions** (i.e. commands to execute when a pattern matches a line).
|
|
|
73
|
|
|
74 The basic form of AWK program is::
|
|
|
75
|
|
|
76 pattern { action 1; action 2; action 3; }
|
|
|
77
|
|
|
78
|
|
|
79 **Pattern Examples**
|
|
|
80
|
|
|
81 - **$2 == "chr3"** will match lines whose second column is the string 'chr3'
|
|
|
82 - **$5-$4>23** will match lines that after subtracting the value of the fourth column from the value of the fifth column, gives value alrger than 23.
|
|
|
83 - **/AG..AG/** will match lines that contain the regular expression **AG..AG** (meaning the characeters AG followed by any two characeters followed by AG). (This is the way to specify regular expressions on the entire line, similar to GREP.)
|
|
|
84 - **$7 ~ /A{4}U/** will match lines whose seventh column contains 4 consecutive A's followed by a U. (This is the way to specify regular expressions on a specific field.)
|
|
6
|
85 - **10000 < $4 && $4 < 20000** will match lines whose fourth column value is larger than 10,000 but smaller than 20,000
|
|
0
|
86 - If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines).
|
|
|
87
|
|
|
88
|
|
|
89 **Action Examples**
|
|
|
90
|
|
|
91 - **{ print }** or **{ print $0 }** will print the entire input line (the line that matched in **pattern**). **$0** is a special marker meaning 'the entire line'.
|
|
|
92 - **{ print $1, $4, $5 }** will print only the first, fourth and fifth fields of the input line.
|
|
|
93 - **{ print $4, $5-$4 }** will print the fourth column and the difference between the fifth and fourth column. (If the fourth column was start-position in the input file, and the fifth column was end-position - the output file will contain the start-position, and the length).
|
|
|
94 - If no action part is specified (not even the curly brackets) - the default action is to print the entire line.
|
|
|
95
|
|
|
96
|
|
|
97 **AWK's Regular Expression Syntax**
|
|
|
98
|
|
7
|
99 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
|
100
|
|
|
101 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
|
|
|
102 - **^** matches the beginning of a string(but not an internal line).
|
|
|
103 - **(** .. **)** groups a particular pattern.
|
|
|
104 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
|
|
|
105
|
|
|
106 - **{n}** The preceding item is matched exactly n times.
|
|
7
|
107 - **{n,}** The preceding item ismatched n or more times.
|
|
|
108 - **{n,m}** The preceding item is matched at least n times but not more than m times.
|
|
0
|
109
|
|
|
110 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
|
|
|
111 - **.** Matches any single character except a newline.
|
|
|
112 - ***** The preceding item will be matched zero or more times.
|
|
|
113 - **?** The preceding item is optional and matched at most once.
|
|
|
114 - **+** The preceding item will be matched one or more times.
|
|
|
115 - **^** has two meaning:
|
|
7
|
116 - matches the beginning of a line or string.
|
|
0
|
117 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
|
|
|
118 - **$** matches the end of a line or string.
|
|
7
|
119 - **\|** Separates alternate possibilities.
|
|
0
|
120
|
|
4
|
121 @REFERENCES@
|
|
|
122 ]]>
|
|
1
|
123 </help>
|
|
0
|
124 </tool>
|
