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1 <tool id="cshl_awk_tool1" name="Awk" version="0.1.1">
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2 <description></description>
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3 <command>
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4 gawk --sandbox -v FS=\$'\t' -v OFS=\$'\t' --re-interval -f '$awk_script' '$input1' > '$output'
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5 </command>
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6 <inputs>
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7 <param format="txt" name="input1" type="data" label="File to process" />
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8
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9 <param name="url_paste" type="text" area="true" size="5x35" label="AWK Program" help="">
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10 <sanitizer>
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11 <valid initial="string.printable">
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12 <remove value="'"/>
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13 </valid>
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14 </sanitizer>
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15 </param>
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16
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17 </inputs>
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18 <outputs>
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19 <data format="input" name="output" metadata_source="input1"
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20 />
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21 </outputs>
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22 <configfiles>
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23 <configfile name="awk_script">
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24 $url_paste
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25 </configfile>
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26 </configfiles>
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27 <help>
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28
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29 **What it does**
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30
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31 This tool runs the unix **awk** command on the selected data file.
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32
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33 .. class:: infomark
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34
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35 **TIP:** This tool uses the **extended regular** expression syntax (not the perl syntax).
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36
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37
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38 **Further reading**
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39
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40 - Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1.html)
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41 - Long AWK tutorial (http://www.grymoire.com/Unix/Awk.html)
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42 - Learn AWK in 1 hour (http://www.selectorweb.com/awk.html)
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43 - awk cheat-sheet (http://cbi.med.harvard.edu/people/peshkin/sb302/awk_cheatsheets.pdf)
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44 - Collection of useful awk one-liners (http://student.northpark.edu/pemente/awk/awk1line.txt)
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45
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46 -----
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47
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48 **AWK programs**
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49
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50 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).
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51
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52 The basic form of AWK program is::
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53
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54 pattern { action 1; action 2; action 3; }
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55
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56
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57
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58
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59
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60 **Pattern Examples**
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61
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62 - **$2 == "chr3"** will match lines whose second column is the string 'chr3'
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63 - **$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.
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64 - **/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.)
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65 - **$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.)
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66 - **10000 < $4 && $4 < 20000** will match lines whose fourth column value is larger than 10,000 but smaller than 20,000
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67 - If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines).
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68
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69
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70
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71 **Action Examples**
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72
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73 - **{ 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'.
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74 - **{ print $1, $4, $5 }** will print only the first, fourth and fifth fields of the input line.
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75 - **{ 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).
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76 - If no action part is specified (not even the curly brackets) - the default action is to print the entire line.
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77
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78
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79
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80
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81
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82
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83
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84
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85
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86 **AWK's Regular Expression Syntax**
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87
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88 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.
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89
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90 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
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91 - **^** matches the beginning of a string(but not an internal line).
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92 - **(** .. **)** groups a particular pattern.
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93 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
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94
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95 - **{n}** The preceding item is matched exactly n times.
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96 - **{n,}** The preceding item ismatched n or more times.
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97 - **{n,m}** The preceding item is matched at least n times but not more than m times.
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98
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99 - **[** ... **]** 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**.
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100 - **.** Matches any single character except a newline.
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101 - ***** The preceding item will be matched zero or more times.
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102 - **?** The preceding item is optional and matched at most once.
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103 - **+** The preceding item will be matched one or more times.
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104 - **^** has two meaning:
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105 - matches the beginning of a line or string.
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106 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
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107 - **$** matches the end of a line or string.
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108 - **\|** Separates alternate possibilities.
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109
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110
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111 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.
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112
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113 </help>
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114 </tool>
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