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comparison awk.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_awk_tool" name="Awk" version="0.1.1">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="4.1.0">gnu_awk</requirement>
5 </requirements>
6 <command>
7 awk --sandbox -v FS=\$'\t' -v OFS=\$'\t' --re-interval -f '$awk_script' '$input' &gt; '$output'
8 </command>
9 <inputs>
10 <param format="txt" name="input" type="data" label="File to process" />
11 <param name="url_paste" type="text" area="true" size="5x35" label="AWK Program" help="">
12 <sanitizer>
13 <valid initial="string.printable">
14 <remove value="&apos;"/>
15 </valid>
16 </sanitizer>
17 </param>
18 </inputs>
19 <tests>
20 <test>
21 <param name="input" value="unix_awk_input1.txt" />
22 <output name="output" file="unix_awk_output1.txt" />
23 <param name="FS" value="tab" />
24 <param name="OFS" value="tab" />
25 <param name="file_data" value="$2>0.5 { print $2*9, $1 }" />
26 </test>
27 </tests>
28 <outputs>
29 <data format="input" name="output" metadata_source="input1"
30 />
31 </outputs>
32 <configfiles>
33 <configfile name="awk_script">
34 $url_paste
35 </configfile>
36 </configfiles>
37 <help>
38
39 **What it does**
40
41 This tool runs the unix **awk** command on the selected data file.
42
43 .. class:: infomark
44
45 **TIP:** This tool uses the **extended regular** expression syntax (not the perl syntax).
46
47
48 **Further reading**
49
50 - Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1.html)
51 - Long AWK tutorial (http://www.grymoire.com/Unix/Awk.html)
52 - Learn AWK in 1 hour (http://www.selectorweb.com/awk.html)
53 - awk cheat-sheet (http://cbi.med.harvard.edu/people/peshkin/sb302/awk_cheatsheets.pdf)
54 - Collection of useful awk one-liners (http://student.northpark.edu/pemente/awk/awk1line.txt)
55
56 -----
57
58 **AWK programs**
59
60 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).
61
62 The basic form of AWK program is::
63
64 pattern { action 1; action 2; action 3; }
65
66
67
68
69
70 **Pattern Examples**
71
72 - **$2 == "chr3"** will match lines whose second column is the string 'chr3'
73 - **$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.
74 - **/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.)
75 - **$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.)
76 - **10000 &lt; $4 &amp;&amp; $4 &lt; 20000** will match lines whose fourth column value is larger than 10,000 but smaller than 20,000
77 - If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines).
78
79
80
81 **Action Examples**
82
83 - **{ 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'.
84 - **{ print $1, $4, $5 }** will print only the first, fourth and fifth fields of the input line.
85 - **{ 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).
86 - If no action part is specified (not even the curly brackets) - the default action is to print the entire line.
87
88
89
90
91
92
93
94
95
96 **AWK's 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 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
101 - **^** matches the beginning of a string(but not an internal line).
102 - **(** .. **)** groups a particular pattern.
103 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
104
105 - **{n}** The preceding item is matched exactly n times.
106 - **{n,}** The preceding item ismatched n or more times.
107 - **{n,m}** The preceding item is matched at least n times but not more than m times.
108
109 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
110 - **.** Matches any single character except a newline.
111 - ***** The preceding item will be matched zero or more times.
112 - **?** The preceding item is optional and matched at most once.
113 - **+** The preceding item will be matched one or more times.
114 - **^** has two meaning:
115 - matches the beginning of a line or string.
116 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
117 - **$** matches the end of a line or string.
118 - **\|** Separates alternate possibilities.
119
120
121 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.
122
123 </help>
124 </tool>