diff fasta_filter_by_length.xml @ 0:16679a7f554a draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_filter_by_length.xml	Mon May 19 12:33:03 2014 -0400
@@ -0,0 +1,56 @@
+<tool id="fasta_filter_by_length" name="Filter sequences by length" version="1.1">
+	<description></description>
+	<command interpreter="python">fasta_filter_by_length.py $input $min_length $max_length $output </command>
+	<inputs>
+		<param name="input" type="data" format="fasta" label="Fasta file"/>
+		<param name="min_length" type="integer" size="15" value="0" label="Minimal length" />
+		<param name="max_length" type="integer" size="15" value="0" label="Maximum length" help="Setting to '0' will return all sequences longer than the 'Minimal length'"/> 
+	</inputs>
+	<outputs>
+		<data name="output" format="fasta"/>
+	</outputs>
+	<tests>
+		<test>
+			<param name="input" value="454.fasta" />
+			<param name="min_length" value="10" />
+			<param name="max_length" value="0" />
+			<output name="output" file="fasta_tool_filter_length_1.out" />
+		</test>
+	</tests>
+	<help>
+
+.. class:: infomark
+
+**TIP**. To return sequences longer than a certain length, set *Minimal length* to desired value and leave *Maximum length* set to '0'.
+
+-----
+
+**What it does**
+	
+Outputs sequences between *Minimal length* and *Maximum length*.
+ 
+-----
+
+**Example**
+
+Suppose you have the following FASTA formatted sequences::
+
+	&gt;seq1
+	TCATTTAATGAC
+	&gt;seq2
+	ATGGC
+	&gt;seq3
+	TCACATGATGCCG
+	&gt;seq4
+	ATGGAAGC
+
+Setting the **Minimal length** to **10**, and the **Maximum length** to **0** will return all sequences longer than 10 bp::
+
+ 	&gt;seq1
+	TCATTTAATGAC
+	&gt;seq3
+	TCACATGATGCCG
+
+
+	</help>
+</tool>
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