diff SMART/galaxy/CompareOverlappingSmallQuery.xml @ 56:97aa2e42bfdf

Uploaded

--- a/SMART/galaxy/CompareOverlappingSmallQuery.xml	Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/galaxy/CompareOverlappingSmallQuery.xml	Wed Feb 05 11:51:11 2014 -0500
@@ -15,6 +15,8 @@
 			-f gff3
 		#elif $formatType.FormatInputFileName1 == 'sam':
 			-f sam
+		#elif $formatType.FormatInputFileName1 == 'bam':
+			-f bam
 		#elif $formatType.FormatInputFileName1 == 'gtf':
 			-f gtf
 		#end if
@@ -29,6 +31,8 @@
 			-g gff3
 		#elif $formatType2.FormatInputFileName2 == 'sam':
 			-g sam
+		#elif $formatType2.FormatInputFileName2 == 'bam':
+			-g bam
 		#elif $formatType2.FormatInputFileName2 == 'gtf':
 		    -g gtf
 		#end if
@@ -64,6 +68,7 @@
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
 				<option value="sam">sam</option>
+				<option value="bam">bam</option>
 				<option value="gtf">gtf</option>
 			</param>
 			<when value="bed">
@@ -81,6 +86,9 @@
 			<when value="sam">
 				<param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
 			</when>
+			<when value="bam">
+				<param name="inputFileName1" format="bam" type="data" label="Input File 1"/>
+			</when>
 			<when value="gtf">
 				<param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
 								                        </when>
@@ -93,6 +101,7 @@
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
 				<option value="sam">sam</option>
+				<option value="bam">bam</option>
 				<option value="gtf">gtf</option>
 			</param>
 			<when value="bed">
@@ -110,6 +119,9 @@
 			<when value="sam">
 				<param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
 			</when>
+			<when value="bam">
+				<param name="inputFileName2" format="bam" type="data" label="Input File 2"/>
+			</when>
 			<when value="gtf">
 				<param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
 			</when>