annotate sed.xml @ 24:c41d78ae5fee draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 4dd118c84ed4d6157303e71438c24446ec4b4f31

<tool id="tp_sed_tool" name="Text transformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>with sed</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <requirements>
        <requirement type="package" version="4.8">sed</requirement>
    </requirements>
    <version_command>sed --version | head -n 1</version_command>
    <command>
<![CDATA[
        sed
            --sandbox
            -r
            #if $adv_opts.adv_opts_selector == 'advanced':
                $adv_opts.silent
            #end if
            -f '$sed_script'
            '$infile'
        > '$output'
]]>
    </command>
    <configfiles>
        <configfile name="sed_script">
          $code
        </configfile>
    </configfiles>
    <inputs>
        <param format="txt" name="infile" type="data" label="File to process" />
        <param name="code" type="text" area="true" size="5x35" label="SED Program" help="">
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
            </sanitizer>
        </param>
        <conditional name="adv_opts">
            <param name="adv_opts_selector" type="select" label="Advanced Options">
              <option value="basic" selected="True">Hide Advanced Options</option>
              <option value="advanced">Show Advanced Options</option>
            </param>
            <when value="basic" />
            <when value="advanced">
                <param name="silent" type="select" label="Operation mode" help="Same as 'sed -n', leave at 'normal' unless you know what you're doing." >
                    <option value="">normal</option>
                    <option value="-n">silent</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format_source="infile" metadata_source="infile" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="sed1.txt" />
            <param name="code" value="1d ; s/foo/bar/" />
            <conditional name="adv_opts">
                <param name="adv_opts_selector" value="advanced" />
                <param name="silent" value="" />
            </conditional>
            <output name="output" file="sed_results1.txt" />
        </test>
        <test>
            <param name="infile" value="sed1.txt" />
            <param name="code" value="/foo/ { s/foo/baz/g ; p }" />
            <conditional name="adv_opts">
                <param name="adv_opts_selector" value="advanced" />
                <param name="silent" value="-n" />
            </conditional>
            <output name="output" file="sed_results2.txt" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

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

.. class:: infomark

**TIP:** This tool uses the **extended regular** expression syntax (same as running 'sed -r').



**Further reading**

- Short sed tutorial (http://www.linuxhowtos.org/System/sed_tutorial.htm)
- Long sed tutorial (http://www.grymoire.com/Unix/Sed.html)
- sed faq with good examples (http://sed.sourceforge.net/sedfaq.html)
- sed cheat-sheet (http://www.catonmat.net/download/sed.stream.editor.cheat.sheet.pdf)

-----

**Sed commands**

The most useful sed command is **s** (substitute).

**Examples**

- **s/hsa//**  will remove the first instance of 'hsa' in every line.
- **s/hsa//g**  will remove all instances (beacuse of the **g**) of 'hsa' in every line.
- **s/A{4,}/--&--/g**  will find sequences of 4 or more consecutive A's, and once found, will surround them with two dashes from each side. The **&** marker is a place holder for 'whatever matched the regular expression'.
- **s/hsa-mir-([^ ]+)/short name: \\1 full name: &/**  will find strings such as 'hsa-mir-43a' (the regular expression is 'hsa-mir-' followed by non-space characters) and will replace it will string such as 'short name: 43a full name: hsa-mir-43a'.  The **\\1** marker is a place holder for 'whatever matched the first parenthesis' (similar to perl's **$1**) .


**sed'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**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.

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