[3] | 1 | <tool id="cshl_awk_tool" name="awk"> |
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| 2 | <description></description> |
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| 3 | <command interpreter="sh">awk_wrapper.sh $input $output '$file_data' '$FS' '$OFS'</command> |
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| 4 | <inputs> |
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| 5 | <param format="txt" name="input" type="data" label="File to process" /> |
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| 6 | |
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| 7 | <param name="FS" type="select" label="Input field-separator"> |
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| 8 | <option value=",">comma (,)</option> |
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| 9 | <option value=":">colons (:) </option> |
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| 10 | <option value=" ">single space</option> |
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| 11 | <option value=".">dot (.)</option> |
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| 12 | <option value="-">dash (-)</option> |
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| 13 | <option value="|">pipe (|)</option> |
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| 14 | <option value="_">underscore (_)</option> |
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| 15 | <option selected="True" value="tab">tab</option> |
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| 16 | </param> |
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| 17 | |
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| 18 | <param name="OFS" type="select" label="Output field-separator"> |
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| 19 | <option value=",">comma (,)</option> |
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| 20 | <option value=":">colons (:)</option> |
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| 21 | <option value=" ">space ( )</option> |
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| 22 | <option value="-">dash (-)</option> |
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| 23 | <option value=".">dot (.)</option> |
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| 24 | <option value="|">pipe (|)</option> |
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| 25 | <option value="_">underscore (_)</option> |
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| 26 | <option selected="True" value="tab">tab</option> |
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| 27 | </param> |
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| 28 | |
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| 29 | |
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| 30 | <!-- Note: the parameter ane MUST BE 'url_paste' - |
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| 31 | This is a hack in the galaxy library (see ./lib/galaxy/util/__init__.py line 142) |
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| 32 | If the name is 'url_paste' the string won't be sanitized, and all the non-alphanumeric characters |
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| 33 | will be passed to the shell script --> |
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| 34 | <param name="file_data" type="text" area="true" size="5x35" label="AWK Program" help=""> |
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| 35 | <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator> |
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| 36 | </param> |
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| 37 | |
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| 38 | </inputs> |
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| 39 | <tests> |
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| 40 | <test> |
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| 41 | <param name="input" value="unix_awk_input1.txt" /> |
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| 42 | <output name="output" file="unix_awk_output1.txt" /> |
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| 43 | <param name="FS" value="tab" /> |
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| 44 | <param name="OFS" value="tab" /> |
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| 45 | <param name="file_data" value="$2>0.5 { print $2*9, $1 }" /> |
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| 46 | </test> |
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| 47 | </tests> |
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| 48 | <outputs> |
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| 49 | <data format="input" name="output" metadata_source="input" /> |
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| 50 | </outputs> |
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| 51 | <help> |
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| 52 | |
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| 53 | **What it does** |
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| 54 | |
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| 55 | This tool runs the unix **awk** command on the selected data file. |
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| 56 | |
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| 57 | .. class:: infomark |
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| 58 | |
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| 59 | **TIP:** This tool uses the **extended regular** expression syntax (not the perl syntax). |
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| 60 | |
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| 61 | |
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| 62 | **Further reading** |
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| 63 | |
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| 64 | - Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1.html) |
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| 65 | - Long AWK tutorial (http://www.grymoire.com/Unix/Awk.html) |
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| 66 | - Learn AWK in 1 hour (http://www.selectorweb.com/awk.html) |
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| 67 | - awk cheat-sheet (http://cbi.med.harvard.edu/people/peshkin/sb302/awk_cheatsheets.pdf) |
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| 68 | - Collection of useful awk one-liners (http://student.northpark.edu/pemente/awk/awk1line.txt) |
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| 69 | |
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| 70 | ----- |
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| 71 | |
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| 72 | **AWK programs** |
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| 73 | |
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| 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). |
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| 75 | |
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| 76 | The basic form of AWK program is:: |
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| 77 | |
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| 78 | pattern { action 1; action 2; action 3; } |
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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 | **Pattern Examples** |
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| 85 | |
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| 86 | - **$2 == "chr3"** will match lines whose second column is the string 'chr3' |
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| 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. |
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| 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.) |
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| 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.) |
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| 90 | - **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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| 91 | - If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines). |
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| 92 | |
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| 93 | |
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| 94 | |
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| 95 | **Action Examples** |
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| 96 | |
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| 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'. |
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| 98 | - **{ print $1, $4, $5 }** will print only the first, fourth and fifth fields of the input line. |
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| 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). |
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| 100 | - If no action part is specified (not even the curly brackets) - the default action is to print the entire line. |
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| 101 | |
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| 102 | |
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| 103 | |
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| 104 | |
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| 105 | |
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| 106 | |
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| 107 | |
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| 108 | |
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| 109 | |
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| 110 | **AWK's Regular Expression Syntax** |
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| 111 | |
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| 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. |
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| 113 | |
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| 114 | - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. |
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| 115 | - **^** matches the beginning of a string(but not an internal line). |
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| 116 | - **(** .. **)** groups a particular pattern. |
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| 117 | - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. |
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| 118 | |
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| 119 | - **{n}** The preceding item is matched exactly n times. |
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| 120 | - **{n,}** The preceding item ismatched n or more times. |
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| 121 | - **{n,m}** The preceding item is matched at least n times but not more than m times. |
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| 122 | |
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| 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**. |
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| 124 | - **.** Matches any single character except a newline. |
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| 125 | - ***** The preceding item will be matched zero or more times. |
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| 126 | - **?** The preceding item is optional and matched at most once. |
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| 127 | - **+** The preceding item will be matched one or more times. |
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| 128 | - **^** has two meaning: |
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| 129 | - matches the beginning of a line or string. |
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| 130 | - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. |
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| 131 | - **$** matches the end of a line or string. |
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| 132 | - **\|** Separates alternate possibilities. |
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| 133 | |
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| 134 | |
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| 135 | **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. |
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| 136 | |
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| 137 | </help> |
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| 138 | </tool> |
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