# HG changeset patch
# User Michael R. Crusoe <mcrusoe@msu.edu>
# Date 1404073355 14400
# Node ID e825c66d31de3731fb62403bb898743a41548a6b
# Parent  c1f0790be1c46f14b9ed6fe9ad074dd3b092356d
filter-abund tests

diff -r c1f0790be1c4 -r e825c66d31de filter-abund.xml
--- a/filter-abund.xml	Sun Jun 29 16:07:06 2014 -0400
+++ b/filter-abund.xml	Sun Jun 29 16:22:35 2014 -0400
@@ -15,6 +15,9 @@
 	<command>
 mkdir output; cd output;
 filter-abund.py
+#if $cutoff != 2
+  --cutoff=$cutoff
+#fi
 $variable_coverage
 $countingtable_to_load
 #for input in $inputs
@@ -31,6 +34,11 @@
 			falsevalue=""
 			label="Variable coverage"
 			help="Only trim when a sequence has high enough coverage (median abundance > 20)" />
+		<param	name="cutoff"
+			type="integer"
+			value="2"
+			label="cutoff"
+			help="Trim at k-mers below this abundance." />
 		<expand macro="input_counting_table_filename" />	
 	</inputs>
 	<outputs>
@@ -41,23 +49,32 @@
 		<exit_code	range="1:"
 				level="fatal" />
 	</stdio>
-    
-    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
-    <tests>
-        <!-- [HELP] Test files have to be in the ~/test-data directory
-        <test>
-            <param name="input" value="input_test.tab" />
-            <param name="int"   value="10" />
-            <output name="output" file="output_test.txt" />
-	</test> -->
-        <!-- [HELP] Multiple tests can be defined with different parameters -->
-<!--
-        <test>
-        </test>
--->
-    </tests>
-    
-    <!-- [OPTIONAL] Help displayed in Galaxy -->
+        <tests>
+                <test>
+                        <param name="inputs" value="test-abund-read-2.fa" />
+                        <param name="input_counting_table_filename" value="test-abund-read-2.ct" />
+                        <output name="output">
+				<discover_dataset name="test-abund-read-2.fa.abundfilt">
+                                	<assert_contents>
+                                        	<has_text text="GGTTGACGGGGCTCAGGG" />
+                                	</assert_contents>
+				</discover_dataset>
+                        </output>
+                </test>
+                <test>
+                        <param name="input_sequence_filename" value="test-abund-read-2.fa" />
+                        <param name="input_counting_table_filename" value="test-abund-read-2.ct" />
+			<param name="cutoff" value="1" />
+                        <output name="output">
+				<discover_dataset name="test-abund-read-2.fa.abundfilt">
+                                	<assert_contents>
+                                        	<has_text text="GGTTGACGGGGCTCAGGG" />
+                                	</assert_contents>
+				</discover_dataset>
+                        </output>
+                </test>
+        </tests> 
+	<!-- [OPTIONAL] Help displayed in Galaxy -->
     <!--
 	<help>
 	</help>