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annotate awk.xml @ 0:224be21ac8c7

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author pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
date Sun, 19 Oct 2014 15:04:49 +0900
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children 69fbeac761c2
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pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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1 <!--
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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2 This tool is based on 'cshl_awk_tool' from Hannon Lab CSHL
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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3 http://hannonlab.cshl.edu/galaxy_unix_tools/
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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4 Thanks. Pitagora
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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5 -->
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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6 <tool id="awk" name="awk">
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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7 <description></description>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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8 <command interpreter="sh">awk_wrapper.sh $input $output '$file_data' '$FS' '$OFS'</command>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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9 <inputs>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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10 <param format="txt" name="input" type="data" label="File to process" />
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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11 <param name="FS" type="select" label="Input field-separator">
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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12 <option value=",">comma (,)</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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13 <option value=":">colons (:) </option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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14 <option value=" ">single space</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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15 <option value=".">dot (.)</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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16 <option value="-">dash (-)</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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17 <option value="|">pipe (|)</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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18 <option value="_">underscore (_)</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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19 <option selected="True" value="tab">tab</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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20 </param>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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21 <param name="OFS" type="select" label="Output field-separator">
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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22 <option value=",">comma (,)</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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23 <option value=":">colons (:)</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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24 <option value=" ">space ( )</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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25 <option value="-">dash (-)</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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26 <option value=".">dot (.)</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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27 <option value="|">pipe (|)</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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28 <option value="_">underscore (_)</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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29 <option selected="True" value="tab">tab</option>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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30 </param>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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31 <param name="file_data" type="text" area="true" size="5x60" label="AWK Program" help="">
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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32 <sanitizer>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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33 <valid initial="string.printable">
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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34 <remove value="&apos;"/>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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35 </valid>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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36 <mapping initial="none">
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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37 <add source="&apos;" target="__sq__"/>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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38 </mapping>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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39 </sanitizer>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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40 </param>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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41 </inputs>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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42 <tests>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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43 <test>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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44 <param name="input" value="unix_awk_input1.txt" />
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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45 <output name="output" file="unix_awk_output1.txt" />
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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46 <param name="FS" value="tab" />
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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47 <param name="OFS" value="tab" />
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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48 <param name="file_data" value="$2>0.5 { print $2*9, $1 }" />
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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49 </test>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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50 </tests>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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51 <outputs>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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52 <data format="input" name="output" metadata_source="input" />
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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53 </outputs>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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54 <help>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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55
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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56 **What it does**
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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57
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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58 This tool runs the unix **awk** command on the selected data file.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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59
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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60 .. class:: infomark
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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61
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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62 **TIP:** This tool uses the **extended regular** expression syntax (not the perl syntax).
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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63
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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64
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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65 **Further reading**
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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66
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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67 - Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1.html)
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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68 - Long AWK tutorial (http://www.grymoire.com/Unix/Awk.html)
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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69 - Learn AWK in 1 hour (http://www.selectorweb.com/awk.html)
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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70 - awk cheat-sheet (http://cbi.med.harvard.edu/people/peshkin/sb302/awk_cheatsheets.pdf)
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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71 - Collection of useful awk one-liners (http://student.northpark.edu/pemente/awk/awk1line.txt)
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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72
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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73 -----
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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74
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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75 **AWK programs**
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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76
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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77 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).
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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78
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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79 The basic form of AWK program is::
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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80
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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81 pattern { action 1; action 2; action 3; }
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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82
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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83
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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84
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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85
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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86
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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87 **Pattern Examples**
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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88
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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89 - **$2 == "chr3"** will match lines whose second column is the string 'chr3'
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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90 - **$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.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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91 - **/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.)
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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92 - **$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.)
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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93 - **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
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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94 - If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines).
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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95
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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96
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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97
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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98 **Action Examples**
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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99
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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100 - **{ 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'.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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101 - **{ print $1, $4, $5 }** will print only the first, fourth and fifth fields of the input line.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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102 - **{ 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).
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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103 - If no action part is specified (not even the curly brackets) - the default action is to print the entire line.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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104
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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105
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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106
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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107
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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108
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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109
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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110
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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111
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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112
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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113 **AWK's Regular Expression Syntax**
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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114
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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115 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.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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116
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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117 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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118 - **^** matches the beginning of a string(but not an internal line).
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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119 - **(** .. **)** groups a particular pattern.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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120 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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121
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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122 - **{n}** The preceding item is matched exactly n times.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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123 - **{n,}** The preceding item ismatched n or more times.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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124 - **{n,m}** The preceding item is matched at least n times but not more than m times.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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125
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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126 - **[** ... **]** 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**.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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127 - **.** Matches any single character except a newline.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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128 - ***** The preceding item will be matched zero or more times.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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129 - **?** The preceding item is optional and matched at most once.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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130 - **+** The preceding item will be matched one or more times.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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131 - **^** has two meaning:
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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132 - matches the beginning of a line or string.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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133 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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134 - **$** matches the end of a line or string.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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135 - **\|** Separates alternate possibilities.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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136
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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137
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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138 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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139
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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140 </help>
pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp>
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141 </tool>