# HG changeset patch
# User Michael R. Crusoe <mcrusoe@msu.edu>
# Date 1404061287 14400
# Node ID de12b461034f02ae08c0199dcd841df4b8012233
# Parent  f2151b15d0b6cce7981ecd779da4eb01b59df8ac
fix nobigcount

diff -r f2151b15d0b6 -r de12b461034f abundance-dist-single.xml
--- a/abundance-dist-single.xml	Sun Jun 29 12:51:01 2014 -0400
+++ b/abundance-dist-single.xml	Sun Jun 29 13:01:27 2014 -0400
@@ -35,12 +35,7 @@
 			type="boolean"
 			label="Save the k-mer counting table(s) in a file"
 			help="" />
-		<param	name="zero"
-			type="boolean"
-			truevalue=""
-			falsevalue="--no-zero"
-			checked="true" 
-			help="Output zero count bins" />
+		<expand macron="input_zero" />
 		<param	name="bigcount"
 			type="boolean"
 			truevalue=""
diff -r f2151b15d0b6 -r de12b461034f abundance-dist.xml
--- a/abundance-dist.xml	Sun Jun 29 12:51:01 2014 -0400
+++ b/abundance-dist.xml	Sun Jun 29 13:01:27 2014 -0400
@@ -17,14 +17,16 @@
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
 mkdir output; cd output;
 @BINARY@
-		$input_counting_table_filename
-		$input_sequence_filename
-		$output_histogram_filename	
+--squash
+$input_counting_table_filename
+$input_sequence_filename
+$output_histogram_filename	
 	</command>
 
 	<inputs>
 		<expand macro="input_sequence_filename" />
 		<expand macro="input_counting_table_filename" />
+		<expand macro="input_zero" />
 	</inputs>
 	<outputs>
 		<expand macro="abundance-histogram-output" />
@@ -49,9 +51,8 @@
 		</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="input_counting_table_filename" value="test-abund-read-2.nobigcount.ct" />
  	                <param name="no_zero" value="false" />
-                    	<param name="no_bigcount" value="false" />
                     	<output name="output_histogram_filename">
                             	<assert_contents>
                                     	<has_text text="1 96 96 0.98" />
diff -r f2151b15d0b6 -r de12b461034f macros.xml
--- a/macros.xml	Sun Jun 29 12:51:01 2014 -0400
+++ b/macros.xml	Sun Jun 29 13:01:27 2014 -0400
@@ -104,4 +104,12 @@
                         <discover_datasets pattern="__name__" directory="output" visible="true"/>
                 </data>
 	</xml>
+	<xml name="input_zero">
+                <param  name="zero"
+                        type="boolean"
+                        truevalue=""
+                        falsevalue="--no-zero"
+                        checked="true" 
+                        help="Output zero count bins" />
+	</xml>
 `</macros>
diff -r f2151b15d0b6 -r de12b461034f test-data/test-abund-read-2.nobigcount.ct
Binary file test-data/test-abund-read-2.nobigcount.ct has changed