--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sort.xml	Thu Sep 05 04:58:21 2013 -0400
@@ -0,0 +1,137 @@
+<tool id="unixtools_sort_header_tool" name="Sort" version="0.1.1">
+    <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="1" 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>
+
+        <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="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>
+    </inputs>
+    <tests>
+    </tests>
+    <outputs>
+        <data format="input" name="outfile" metadata_source="infile"/>
+    </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>