# HG changeset patch
# User m-zytnicki
# Date 1445248949 -7200
# Node ID 5f210bc9f486eb967d8f1e8566da8d046f4cdc92
# Parent  8c42a6d7ffd4ac5204bf7c3def97df7e9963ed24
Added a simple test for Clusterize

diff -r 8c42a6d7ffd4 -r 5f210bc9f486 .hgignore
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.hgignore	Mon Oct 19 12:02:29 2015 +0200
@@ -0,0 +1,2 @@
+syntax: glob
+.*.swp
diff -r 8c42a6d7ffd4 -r 5f210bc9f486 SMART/galaxy/.Clusterize.xml.swp
Binary file SMART/galaxy/.Clusterize.xml.swp has changed
diff -r 8c42a6d7ffd4 -r 5f210bc9f486 SMART/galaxy/Clusterize.xml
--- a/SMART/galaxy/Clusterize.xml	Mon Oct 19 11:25:11 2015 +0200
+++ b/SMART/galaxy/Clusterize.xml	Mon Oct 19 12:02:29 2015 +0200
@@ -51,6 +51,18 @@
 		<data name="outputFileGff" format="gff3"/>
 	</outputs> 
 
+    <tests>
+        <test>
+            <!-- basic test -->
+            <param name="FormatInputFileName" value="bed"/>
+            <param name="inputFileName" value="smart_1.bed" ftype="bed"/>
+            <param name="colinear" value="false"/>
+            <param name="normalize" value="false"/>
+            <param name="distance" value="0"/>
+            <output name="output" file="smart_clusterize_out_1.gff3" ftype="gff3"/>
+        </test>
+    </tests>
+
 	<help>
 The script clusterizes the input genomic data. Two features are clusterized when their genomic intervals overlap. The output is a GFF3 file, where each element is a cluster. The number of elements in the cluster is given by the tag **nbElements**. The name of a cluster is the concatation of the names of its reads (like **read1--read2--read3**). Note that if the size of the name of the cluster exceeds 100 characters, it is truncated to the first 100 characters.
 
diff -r 8c42a6d7ffd4 -r 5f210bc9f486 test-data/smart_1.bed
--- a/test-data/smart_1.bed	Mon Oct 19 11:25:11 2015 +0200
+++ b/test-data/smart_1.bed	Mon Oct 19 12:02:29 2015 +0200
@@ -1,2 +1,2 @@
-chr1	1000	5000	test1	1000	+
-chr1	2000	6000	test2	1000	-
+chr1	1000	5000	test1
+chr1	2000	6000	test2
diff -r 8c42a6d7ffd4 -r 5f210bc9f486 test-data/smart_clusterize_out_1.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/smart_clusterize_out_1.gff3	Mon Oct 19 12:02:29 2015 +0200
@@ -0,0 +1,1 @@
+chr1	S-MART	transcript	1000	5999	.	+	.	nbElements=2.000000;ID=test2--test1;Name=test2--test1