changeset 63:5f210bc9f486

Added a simple test for Clusterize
author m-zytnicki
date Mon, 19 Oct 2015 12:02:29 +0200
parents 8c42a6d7ffd4
children 783e6ed4eb66 4ab9c86890ba
files .hgignore SMART/galaxy/.Clusterize.xml.swp SMART/galaxy/Clusterize.xml test-data/smart_1.bed test-data/smart_clusterize_out_1.gff3
diffstat 5 files changed, 17 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- /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
Binary file SMART/galaxy/.Clusterize.xml.swp has changed
--- 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.
 
--- 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
--- /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