diff tools/fastq/fastq_paired_unpaired.xml @ 2:95a632a71951 draft

Uploaded v0.0.6, adds unit test

--- a/tools/fastq/fastq_paired_unpaired.xml	Mon Dec 12 11:33:10 2011 -0500
+++ b/tools/fastq/fastq_paired_unpaired.xml	Tue Apr 30 14:08:37 2013 -0400
@@ -1,5 +1,6 @@
-<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.5">
+<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.6">
 	<description>using the read name suffices</description>
+	<version_command interpreter="python">fastq_paired_unpaired.py --version</version_command>
 	<command interpreter="python">
 fastq_paired_unpaired.py $input_fastq.extension $input_fastq
 #if $output_choice_cond.output_choice=="separate"
@@ -9,6 +10,11 @@
 #end if
 $output_singles
 	</command>
+	<stdio>
+		<!-- Anything other than zero is an error -->
+		<exit_code range="1:" />
+		<exit_code range=":-1" />
+	</stdio>
 	<inputs>
 		<param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/>
 		<conditional name="output_choice_cond">
@@ -34,10 +40,20 @@
 		</data>
 	</outputs>
 	<tests>
+		<test>
+			<param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/>
+			<param name="output_choice" value="separate"/>
+			<output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/>
+			<output name="output_forward" file="sanger-pairs-forward.fastq" ftype="fastq"/>
+			<output name="output_reverse" file="sanger-pairs-reverse.fastq" ftype="fastq"/>
+		</test>
+		<test>
+			<param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/>
+			<param name="output_choice" value="interleaved"/>
+			<output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/>
+			<output name="output_paired" file="sanger-pairs-interleaved.fastq" ftype="fastq"/>
+		</test>
 	</tests>
-	<requirements>
-		<requirement type="python-module">Bio</requirement>
-	</requirements>
 	<help>
 
 **What it does**