diff sickle.xml @ 6:c6a790326d1e

moved from test
author nilesh
date Mon, 15 Jul 2013 12:12:41 -0500
parents 98e35d7ce5c9
children dd2ec1b37e96
line wrap: on
line diff
--- a/sickle.xml	Fri Jul 12 14:01:18 2013 -0500
+++ b/sickle.xml	Mon Jul 15 12:12:41 2013 -0500
@@ -1,7 +1,6 @@
 <tool id="sickle" name="Sickle">
 	<description>Windowed Adaptive Trimming of FastQ data</description>
 	<requirements>
-		<requirement type="package" version="1.2.8">zlib</requirement>
 		<requirement type="package" version="1.21.0">sickle</requirement>
 	</requirements>
 	<command>
@@ -84,7 +83,20 @@
 		<filter>(readtype['single_or_paired'] == 'pe')</filter>
 		</data>
 	</outputs>
-
+	<tests>
+		<param name="single_or_paired" value="pe"/>
+		<param name="input_paired1" value="test.f.fastq"/>
+		<param name="input_paired2" value="test.r.fastq"/>
+		<param name="qual_type" value="illumina"/>
+		<param name="qual_threshold" value="20"/>
+		<param name="length_threshold" value="20"/>
+		<param name="no_five_prime" value="false"/>
+		<param name="discard_n" value="false"/>
+		<output name="output_paired1" value="output.f.fastq"/>
+		<output name="output_paired2" value="output.r.fastq"/>
+		<output name="output_paired_single" value="output.fastq"/>
+	</tests>
+	
 	<help>
 Most modern sequencing technologies produce reads that have deteriorating quality towards the 3'-end and some towards the 5'-end as well. Incorrectly called bases in both regions negatively impact assembles, mapping, and downstream bioinformatics analyses.