diff flaimapper.xml @ 24:bd695d4cb7c4 draft

Uploaded

--- a/flaimapper.xml	Wed Mar 25 16:19:39 2015 -0400
+++ b/flaimapper.xml	Sun Mar 29 02:43:11 2015 -0400
@@ -21,6 +21,9 @@
 		#end for
 	</command>
 	
+	<stdio>
+	</stdio>
+	
 	<inputs>
 		<param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" />
 		
@@ -29,10 +32,10 @@
 		<param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
 		
 		<param name="output_format" type="select" label="Output format">
-		<option value="1">Tabular (1 fragment per column)</option>
-		<option value="2">Tabular (1 precursor per column)</option>
-		<option value="3">GenBank</option>
-		<!-- option value="gtf">GTF/GFF</option -->
+			<option value="1">Tabular (1 fragment per column)</option>
+			<option value="2">Tabular (1 precursor per column)</option>
+			<option value="3">GenBank</option>
+			<!-- option value="gtf">GTF/GFF</option -->
 		</param>
 	</inputs>
 	
@@ -40,6 +43,17 @@
 		<data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
 	</outputs>
 	
+	<tests>
+		<test>
+			<param name="alignments" value="snord81.bam" />
+			<param name="mask" value="ncrnadb09.gtf" format="gtf" />
+			<param name="fasta" value="ncrnadb09.fa" format="fasta" />
+			<param name="output_format" value="1" />
+			
+			<output name="output" file="snord81.flaimapper.txt" />
+		</test>
+	</tests>
+	
 	<help>
 FlaiMapper wrapper for Galaxy
 =============================