diff tools/unix_tools/sort_tool.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/unix_tools/sort_tool.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,134 @@
+<tool id="cshl_sort_tool" name="Sort">
+  <!-- 
+   	note 1:
+	  the 'version' sort (or natual order sort)
+	  requires GNU Coreutils 7.1 or later
+
+	note 2:
+	  for greater efficiency, sort buffer size is very large.
+	  If your Galaxy server doesn't have so much memory (or the
+	  sorts you use don't require it) - you can decrease the memory size.
+	  (argument is "-S 2G")
+  -->
+  <command>sort -S 2G $unique 
+      #for $key in $sortkeys
+       '-k ${key.column},${key.column}${key.order}${key.style}'
+      #end for
+  	$input > $out_file1
+  </command>
+
+  <inputs>
+	<param format="txt" name="input" type="data" label="Sort Query" />
+		
+	<param name="unique" type="select" label="Output only unique values?">
+		<option value="">No</option>
+		<option value="-u">Yes</option>
+	</param>
+
+	<repeat name="sortkeys" title="sort key">
+	    <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true" />
+	    <param name="order" type="select" display="radio" label="in">
+	      <option value="r">Descending order</option>
+	      <option value="">Ascending 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>
+	    </param>
+	</repeat>
+  </inputs>
+  <tests>
+	  <test>
+		  <!-- Sort Descending numerical order,
+		       with scientific notation -->
+		  <param name="input" value="unix_sort_input1.txt" />
+		  <output name="output" file="unix_sort_output1.txt" />
+		  <param name="unique" value="No" />
+		  <param name="column" value="2" />
+		  <param name="order"  value="r" />
+		  <param name="style"  value="g" />
+	  </test>
+	  <test>
+		  <!-- Sort Ascending numerical order,
+		  with scientific notation - outputing unique values only 
+
+		  The catch:
+		  	chr15 appears twice, with the same value (0.0314 and 3.14e-2).
+			In the output, it should appear only once because of the unique flag
+		  -->
+		  <param name="input" value="unix_sort_input1.txt" />
+		  <output name="output" file="unix_sort_output2.txt" />
+		  <param name="unique" value="Yes" />
+		  <param name="column" value="2" />
+		  <param name="order"  value="" />
+		  <param name="style"  value="g" />
+	  </test>
+	  <test>
+		  <!-- Sort Ascending 'natural' order -->
+		  <param name="input" value="unix_sort_input1.txt" />
+		  <output name="output" file="unix_sort_output3.txt" />
+		  <param name="unique" value="No" />
+		  <param name="column" value="1" />
+		  <param name="order"  value="" />
+		  <param name="style"  value="V" />
+	  </test>
+  </tests>
+  <outputs>
+    <data format="input" name="out_file1" metadata_source="input"/>
+  </outputs>
+  <help>
+
+**What it does**
+
+This tool runs the unix **sort** command on the selected data 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.
+
+
+
+
+**Sorting Examples**
+
+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.
+
+  </help>
+</tool>