annotate awk.xml @ 22:3dc70b59608c draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b

<tool id="tp_awk_tool" name="Text reformatting" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>with awk</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <requirements>
        <requirement type="package" version="5.3.1">gawk</requirement>
    </requirements>
    <version_command>awk --version | head -n 1</version_command>
    <command>
<![CDATA[
        env -i
        \$(which awk)
            --sandbox
            -v FS='	'
            -v OFS='	'
            --re-interval
            -f '$awk_script'
            '$infile'
        > '$outfile'
]]>
    </command>
    <configfiles>
        <configfile name="awk_script">$code</configfile>
    </configfiles>
    <inputs>
        <param name="infile" format="txt" type="data" label="File to process" />
        <param name="code" type="text" area="true" size="5x35" label="AWK Program" help="">
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
            </sanitizer>
        </param>
    </inputs>
    <outputs>
        <data name="outfile" format_source="infile" metadata_source="infile"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="awk1.txt" />
            <!-- commas are not allowed in a value field. Values with comma will be splitted -->
            <param name="code" value='$2>0.5 { print $2*9"\t"$1 }' />
            <output name="outfile" file="awk_results1.txt" />
        </test>
    </tests>
    <help>
<![CDATA[
**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).
**\\d**, **\\w**, **\\s** etc. are **not** supported.


**Further reading**

- Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1/index.html)
- Long AWK tutorial (http://www.grymoire.com/Unix/Awk.html)

-----

**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 < $4 && $4 < 20000** will match lines whose fourth column value is larger than 10,000 but smaller than 20,000
- **BEGIN** will be executed once only, before the first input record is read.
- 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).
- **{ FS = "," }** can be used to change the field separator (delimeter) for parsing the input file.
- 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.

]]>
  </help>
  <expand macro="citations" />
</tool>