|
0
|
1 <tool id="cshl_awk_tool" name="awk">
|
|
|
2 <description></description>
|
|
|
3 <command interpreter="sh">awk_wrapper.sh $input $output '$file_data' '$FS' '$OFS'</command>
|
|
|
4 <inputs>
|
|
|
5 <param format="txt" name="input" type="data" label="File to process" />
|
|
|
6
|
|
|
7 <param name="FS" type="select" label="Input field-separator">
|
|
|
8 <option value=",">comma (,)</option>
|
|
|
9 <option value=":">colons (:) </option>
|
|
|
10 <option value=" ">single space</option>
|
|
|
11 <option value=".">dot (.)</option>
|
|
|
12 <option value="-">dash (-)</option>
|
|
|
13 <option value="|">pipe (|)</option>
|
|
|
14 <option value="_">underscore (_)</option>
|
|
|
15 <option selected="True" value="tab">tab</option>
|
|
|
16 </param>
|
|
|
17
|
|
|
18 <param name="OFS" type="select" label="Output field-separator">
|
|
|
19 <option value=",">comma (,)</option>
|
|
|
20 <option value=":">colons (:)</option>
|
|
|
21 <option value=" ">space ( )</option>
|
|
|
22 <option value="-">dash (-)</option>
|
|
|
23 <option value=".">dot (.)</option>
|
|
|
24 <option value="|">pipe (|)</option>
|
|
|
25 <option value="_">underscore (_)</option>
|
|
|
26 <option selected="True" value="tab">tab</option>
|
|
|
27 </param>
|
|
|
28
|
|
|
29
|
|
|
30 <!-- Note: the parameter ane MUST BE 'url_paste' -
|
|
|
31 This is a hack in the galaxy library (see ./lib/galaxy/util/__init__.py line 142)
|
|
|
32 If the name is 'url_paste' the string won't be sanitized, and all the non-alphanumeric characters
|
|
|
33 will be passed to the shell script -->
|
|
|
34 <param name="file_data" type="text" area="true" size="5x35" label="AWK Program" help="">
|
|
|
35 <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator>
|
|
|
36 </param>
|
|
|
37
|
|
|
38 </inputs>
|
|
|
39 <tests>
|
|
|
40 <test>
|
|
|
41 <param name="input" value="unix_awk_input1.txt" />
|
|
|
42 <output name="output" file="unix_awk_output1.txt" />
|
|
|
43 <param name="FS" value="tab" />
|
|
|
44 <param name="OFS" value="tab" />
|
|
|
45 <param name="file_data" value="$2>0.5 { print $2*9, $1 }" />
|
|
|
46 </test>
|
|
|
47 </tests>
|
|
|
48 <outputs>
|
|
|
49 <data format="input" name="output" metadata_source="input" />
|
|
|
50 </outputs>
|
|
|
51 <help>
|
|
|
52
|
|
|
53 **What it does**
|
|
|
54
|
|
|
55 This tool runs the unix **awk** command on the selected data file.
|
|
|
56
|
|
|
57 .. class:: infomark
|
|
|
58
|
|
|
59 **TIP:** This tool uses the **extended regular** expression syntax (not the perl syntax).
|
|
|
60
|
|
|
61
|
|
|
62 **Further reading**
|
|
|
63
|
|
|
64 - Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1.html)
|
|
|
65 - Long AWK tutorial (http://www.grymoire.com/Unix/Awk.html)
|
|
|
66 - Learn AWK in 1 hour (http://www.selectorweb.com/awk.html)
|
|
|
67 - awk cheat-sheet (http://cbi.med.harvard.edu/people/peshkin/sb302/awk_cheatsheets.pdf)
|
|
|
68 - Collection of useful awk one-liners (http://student.northpark.edu/pemente/awk/awk1line.txt)
|
|
|
69
|
|
|
70 -----
|
|
|
71
|
|
|
72 **AWK programs**
|
|
|
73
|
|
|
74 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).
|
|
|
75
|
|
|
76 The basic form of AWK program is::
|
|
|
77
|
|
|
78 pattern { action 1; action 2; action 3; }
|
|
|
79
|
|
|
80
|
|
|
81
|
|
|
82
|
|
|
83
|
|
|
84 **Pattern Examples**
|
|
|
85
|
|
|
86 - **$2 == "chr3"** will match lines whose second column is the string 'chr3'
|
|
|
87 - **$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.
|
|
|
88 - **/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.)
|
|
|
89 - **$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.)
|
|
|
90 - **10000 < $4 && $4 < 20000** will match lines whose fourth column value is larger than 10,000 but smaller than 20,000
|
|
|
91 - If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines).
|
|
|
92
|
|
|
93
|
|
|
94
|
|
|
95 **Action Examples**
|
|
|
96
|
|
|
97 - **{ 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'.
|
|
|
98 - **{ print $1, $4, $5 }** will print only the first, fourth and fifth fields of the input line.
|
|
|
99 - **{ 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).
|
|
|
100 - If no action part is specified (not even the curly brackets) - the default action is to print the entire line.
|
|
|
101
|
|
|
102
|
|
|
103
|
|
|
104
|
|
|
105
|
|
|
106
|
|
|
107
|
|
|
108
|
|
|
109
|
|
|
110 **AWK's 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 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
|
|
|
115 - **^** matches the beginning of a string(but not an internal line).
|
|
|
116 - **(** .. **)** groups a particular pattern.
|
|
|
117 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
|
|
|
118
|
|
|
119 - **{n}** The preceding item is matched exactly n times.
|
|
|
120 - **{n,}** The preceding item ismatched n or more times.
|
|
|
121 - **{n,m}** The preceding item is matched at least n times but not more than m times.
|
|
|
122
|
|
|
123 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
|
|
|
124 - **.** Matches any single character except a newline.
|
|
|
125 - ***** The preceding item will be matched zero or more times.
|
|
|
126 - **?** The preceding item is optional and matched at most once.
|
|
|
127 - **+** The preceding item will be matched one or more times.
|
|
|
128 - **^** has two meaning:
|
|
|
129 - matches the beginning of a line or string.
|
|
|
130 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
|
|
|
131 - **$** matches the end of a line or string.
|
|
|
132 - **\|** Separates alternate possibilities.
|
|
|
133
|
|
|
134
|
|
|
135 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.
|
|
|
136
|
|
|
137 </help>
|
|
|
138 </tool>
|
