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

First tool-shed public version

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sort-header.xml	Tue Oct 09 18:48:06 2012 -0400
@@ -0,0 +1,129 @@
+<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>