comparison awk.xml @ 0:631dfde45073 draft default tip

First tool-shed public version

0:631dfde45073

<tool id="cshl_awk_tool1" name="Awk" version="0.1.1">
  <description></description>
  <command>
	gawk --sandbox -v FS=\$'\t' -v OFS=\$'\t' --re-interval -f '$awk_script' '$input1' &gt; '$output'
  </command>
  <inputs>
    <param format="txt" name="input1" type="data" label="File to process" />

    <param name="url_paste" type="text" area="true" size="5x35" label="AWK Program" help="">
	    <sanitizer>
		    <valid initial="string.printable">
			    <remove value="&apos;"/>
		    </valid>
	    </sanitizer>
    </param>

  </inputs>
  <outputs>
	<data format="input" name="output" metadata_source="input1"
	/>
  </outputs>
  <configfiles>
	  <configfile name="awk_script">
		  $url_paste
	</configfile>
  </configfiles>
<help>

**What it does**

This tool runs the unix **awk** command on the selected data file.

.. class:: infomark

**TIP:** This tool uses the **extended regular** expression syntax (not the perl syntax).


**Further reading**

- Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1.html)
- Long AWK tutorial (http://www.grymoire.com/Unix/Awk.html)
- Learn AWK in 1 hour (http://www.selectorweb.com/awk.html)
- awk cheat-sheet (http://cbi.med.harvard.edu/people/peshkin/sb302/awk_cheatsheets.pdf)
- Collection of useful awk one-liners (http://student.northpark.edu/pemente/awk/awk1line.txt)

-----

**AWK programs**

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).

The basic form of AWK program is::

    pattern { action 1; action 2; action 3; }





**Pattern Examples**

- **$2 == "chr3"**  will match lines whose second column is the string 'chr3'
- **$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.
- **/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.)
- **$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.)
- **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
- If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines).



**Action Examples**

- **{ 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'.
- **{ print $1, $4, $5 }** will print only the first, fourth and fifth fields of the input line.
- **{ 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).
- If no action part is specified (not even the curly brackets) - the default action is to print the entire line.









**AWK's Regular Expression Syntax**

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. 

- **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
- **^** matches the beginning of a string(but not an internal line).
- **(** .. **)** groups a particular pattern.
- **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.

  - **{n}** The preceding item is matched exactly n times.
  - **{n,}** The preceding item ismatched n or more times. 
  - **{n,m}** The preceding item is matched at least n times but not more than m times. 

- **[** ... **]** 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**.
- **.** Matches any single character except a newline.
- ***** The preceding item will be matched zero or more times.
- **?** The preceding item is optional and matched at most once.
- **+** The preceding item will be matched one or more times.
- **^** has two meaning:
  - matches the beginning of a line or string. 
  - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
- **$** matches the end of a line or string.
- **\|** Separates alternate possibilities. 


**Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.

</help>
</tool>