view sort-header.xml @ 0:631dfde45073 draft default tip

First tool-shed public version

<tool id="cshl_sort_header" name="Sort" version="0.1.1">
	<command interpreter="perl">sort-header
		--header $header
		$unique
		$ignore_case
		--stable
		-t '	'
		#for $key in $sortkeys
		'-k ${key.column}${key.order}${key.style},${key.column}'
		#end for
		--output '$out_file1'
		'$input1'
	</command>

  <inputs>
	<param format="txt" name="input1" type="data" label="Sort Query" />

	<!-- header line is boolean for now, but the values are 1 or 0.
	     in the future, we can use Galaxy's number-of-comment-lines variable -->
	<param name="header" type="boolean" checked="false" truevalue="1" falsevalue="0"
		label="First line is a header line" help="Use if first line contains column headers. It will not be sorted." />

	<param name="unique" type="boolean" checked="false" truevalue="--unique" falsevalue=""
		label="Output unique values" help="Print only unique values (based on sorted key columns. See help section for details." />

	<param name="ignore_case" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Ignore case" help="Sort and Join key column values regardless of upper/lower case letters." />

	<repeat name="sortkeys" title="sort key">
	    <param name="column" label="on column" type="data_column" data_ref="input1" accept_default="true" />
	    <param name="order" type="select" display="radio" label="in">
	      <option value="">Ascending order</option>
	      <option value="r">Descending order</option>
	    </param>
	    <param name="style" type="select" display="radio" label="Flavor">
	      <option value="n">Fast numeric sort ([-n])</option>
	      <option value="g">General numeric sort ( scientific notation [-g])</option>
	      <option value="V">Natural/Version sort ([-V]) </option>
	      <option value="">Alphabetical sort</option>
	      <option value="h">Human-readable numbers (-h)</option>
	      <option value="R">Random order</option>
	    </param>
	</repeat>
  </inputs>
  <tests>
  </tests>
  <outputs>
    <data format="input" name="out_file1" metadata_source="input1"
	/>
  </outputs>
  <help>

**What it does**

This tool sorts an input file.

-----

**Sorting Styles**

* **Fast Numeric**: sort by numeric values. Handles integer values (e.g. 43, 134) and decimal-point values (e.g. 3.14). *Does not* handle scientific notation (e.g. -2.32e2).
* **General Numeric**: sort by numeric values. Handles all numeric notations (including scientific notation). Slower than *fast numeric*, so use only when necessary.
* **Natural Sort**: Sort in 'natural' order (natural to humans, not to computers). See example below.
* **Alphabetical sort**: Sort in strict alphabetical order. See example below.
* **Human-readable numbers**: Sort human readble numbers (e.g. 1G > 2M > 3K > 400)
* **Random order**: return lines in random order.

------

**Example - Header line**

**Input file** (note first line is a header line, should not be sorted)::

    Fruit   Color   Price
    Banana  Yellow  4.1
    Avocado Green   8.0
    Apple   Red     3.0
    Melon   Green   6.1

**Sorting** by **numeric order** on column **3**, with **header**, will return::

    Fruit   Color   Price
    Apple   Red     3.0
    Banana  Yellow  4.1
    Melon   Green   6.1
    Avocado Green   8.0


-----

**Example - Natural vs. Alphabetical sorting**

Given the following list::

    chr4
    chr13
    chr1
    chr10
    chr20
    chr2

**Alphabetical sort** would produce the following sorted list::

    chr1
    chr10
    chr13
    chr2
    chr20
    chr4

**Natural Sort** would produce the following sorted list::

    chr1
    chr2
    chr4
    chr10
    chr13
    chr20


.. class:: infomark

If you're planning to use the file with another tool that expected sorted files (such as *join*), you should use the **Alphabetical sort**,  not the **Natural Sort**. Natural sort order is easier for humans, but is unnatural for computer programs.

-----

*sort-header* is was written by A. Gordon ( gordon at cshl dot edu )

  </help>
</tool>