view sort.xml @ 1:a4ad586d1403 draft

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<tool id="unixtools_sort_header_tool" name="Sort" version="0.1.1">
    <description>data in ascending or descending order</description>
    <requirements>
        <requirement type="package" version="8.21">gnu_coreutils</requirement>
        <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement>
    </requirements>
    <command interpreter="sh">
        #if int($header) > 0:
            (sed -u '${header}'q &amp;&amp; sort $unique $ignore_case --stable -t '	'

                #for $key in $sortkeys
                '-k ${key.column}${key.order}${key.style},${key.column}'
                #end for

            ) &lt; '${infile}' &gt; '${outfile}'
        #else:
            (sort $unique $ignore_case --stable -t '	' 

                #for $key in $sortkeys
                '-k ${key.column}${key.order}${key.style},${key.column}'
                #end for

            ) &lt; '${infile}' &gt; '${outfile}'
        #end if
    </command>

    <inputs>
        <param format="txt" name="infile" type="data" label="Sort Query" />
        <param name="header" type="integer" size="5" value="0" label="Number of header lines" help="These will be ignored during sort.">
            <validator type="in_range" message="Negative values are not allowed." min="0"/>
        </param>

        <repeat name="sortkeys" title="Column selections" min="1">
            <param name="column" label="on column" type="data_column" data_ref="infile" 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>

        <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." />

    </inputs>
    <outputs>
        <data format="input" name="outfile" metadata_source="infile"/>
    </outputs>
    <tests>
        <!-- anyone knows how to write tests with repeat tags -->
        <test>
            <param name="infile" value="sort_in1.bed"/>
            <param name="column" value="1"/>
            <param name="style" value=""/>
            <param name="order" value="ASC"/>
            <param name="other_column" value="3"/>
            <param name="other_style" value="n"/>
            <param name="other_order" value="r"/>
            <output name="out_file1" file="sort_out1.bed"/>
        </test>
        <test>
            <param name="infile" value="sort_in1.bed"/>
            <param name="column" value="1"/>
            <param name="style" value=""/>
            <param name="order" value="ASC"/>
            <param name="other_column" value="3"/>
            <param name="other_style" value="n"/>
            <param name="other_order" value=""/>
            <output name="out_file1" file="sort_out2.bed"/>
        </test>
        <test>
            <param name="infile" value="sort_in2.bed"/>
            <param name="column" value="5"/>
            <param name="style" value="g"/>
            <param name="order" value=""/>
            <output name="out_file1" file="sort_out3.bed"/>
        </test>
    </tests>
    <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>